Config reference: renderer parameters

The keys a plots.<panel> block of a project config can hold, per renderer, from each renderer's SCHEMA (the same descriptions fa ingest bundle and fa param scaffold write into configs). auto means unset: the renderer decides (e.g. axis limits from the data); computed means the renderer derives it from other values. Units: pt = points (1 pt = 0.35 mm), mm on the page, data coords = the axis's own units.

Plot name	Where	Parameters
bar_scatter	core	50
binary_motif_heatmap	fig_atlas_omics.renderers	62
boxplot	core	13
chromosome_ideogram	fig_atlas_omics.renderers	42
cis_linkage_panel	fig_atlas_omics.renderers	20
clustered_go_heatmap	fig_atlas_omics.renderers	21
count_summary	fig_atlas_omics.renderers	20
cross_condition_dotplot	fig_atlas_omics.renderers	62
cross_condition_heatmap	fig_atlas_omics.renderers	42
dose_response	core	37
dot_matrix	core	42
effect_dots	core	38
flow_diagram	core	44
funnel	core	16
gene_model_track	fig_atlas_omics.renderers	25
go_bar	fig_atlas_omics.renderers	25
go_cluster_dot	fig_atlas_omics.renderers	37
go_dot	fig_atlas_omics.renderers	11
go_rrvgo_treemap	fig_atlas_omics.renderers	14
group_scatter	core	37
grouped_hbar	core	19
heatmap	core	23
histogram	core	33
image_panel	core	27
interval_track	fig_atlas_omics.renderers	33
jaccard_heatmap	core	25
line_band	core	44
ma_plot	fig_atlas_omics.renderers	24
motif_architecture_table	fig_atlas_omics.renderers	5
motif_dotplot	fig_atlas_omics.renderers	44
multi_group_heatmap	core	32
paired_dumbbell	core	39
pathway_evidence_dotplot	fig_atlas_omics.renderers	28
pathway_test_matrix	fig_atlas_omics.renderers	42
pca	core	16
peak_feature_composition	fig_atlas_omics.renderers	32
peak_feature_enrichment	fig_atlas_omics.renderers	32
sample_metric_bars	core	22
segment_array	fig_atlas_omics.renderers	66
signed_heatmap	core	34
single_tf_expression_scatter_bar	fig_atlas_omics.renderers	36
species_response_scatter	fig_atlas_omics.renderers	30
stacked_bar	core	32
stacked_share_hbar	core	28
survival	core	32
tf_expression_scatter_grid	fig_atlas_omics.renderers	36
threshold_scatter	core	61
tier_hbar	core	16
treatment_schematic	core	25
ts_profile	core	18
two_set_euler	core	27
venn	core	5
violin	core	39
volcano	fig_atlas_omics.renderers	28

bar_scatter

fig_atlas.renderers:render_bar_scatter

Key	Type	Default	Unit	What it does
category_col	text	symbol		Column holding the x categories
category_order	list	auto		Category order, left to right (default: order in the data)
groups	list	[]		Wide table: series per category, a list of {label, color, columns} (replicate columns)
group_col	text	auto		Long table (one row per replicate): column with the series; then value_col holds the values and groups is built from group_order/group_colors/group_labels
value_col	text	value		Long table: column with the replicate values
group_order	list	auto		Long table: series order (default: order in the data)
group_colors	mapping	{}	hex color	Long table: bar colour per series
group_labels	mapping	{}		Long table: legend label per series
pvalue_col	text	auto		Column with the per-category p-value for the two-group bracket
bar_width	number	0.8	x units (one category = 1)	Total width of one category's bars
bar_edgecolor	colour	none	color	Bar outline colour
bar_edgewidth	number	0.0	pt	Bar outline width
errorbar	one of sem, sd	sem		Error bar: standard error or standard deviation
errorbar_width	number	1.0	pt	Error bar and cap line width
capsize	number	3.0	pt	Error bar cap length
show_points	true / false	True		Overlay the replicate values as dots
point_color	colour	#111111	hex color	Replicate dot colour
point_edgecolor	colour	white	color	Replicate dot outline
point_edgewidth	number	0.4	pt	Replicate dot outline width
point_size	number	20	pt^2 (marker area)	Replicate dot size
point_jitter	number	0.06	x units	Horizontal jitter of the dots
point_seed	integer	0	random seed	Seed of the jitter (fixed for reproducible output)
show_significance	true / false	True		Draw the star bracket when there are exactly two groups
sig_thresholds	list	[[0.001, '***'], [0.01, '**'], [0.05, '*']]	p-value	[threshold, symbol] pairs, ascending
sig_ns_display	text	ns		Text for non-significant pairs (empty to hide)
sig_font_size	number	computed	pt	Star size (default tick_label_size + 1)
sig_gap	number	0.03	fraction of the data top	Gap between bars and bracket
sig_line_color	colour	#333333	hex color	Bracket line colour
sig_line_width	number	1.0	pt	Bracket line width
y_min	number	0	data coords	Lower y limit
y_max	number	auto	data coords	Upper y limit (default: data top x y_headroom)
y_headroom	number	1.28	multiple of the data top	Space above the bars for the brackets — raise if stars touch the top
grid	true / false	True		Draw horizontal grid lines
grid_alpha	number	0.3	alpha [0-1]	Grid line opacity
despine	true / false	True		Hide the top and right spines
xtick_rotation	number	0	degrees	Category label rotation
xtick_mode	one of category, group	category		x tick labels: one per category, or one per bar named by its group (e.g. a single two-group comparison)
show_legend	true / false	True		Show the group legend
legend_loc	text	upper right		Legend location (matplotlib loc string)
legend_ncol	integer	1	columns	Legend columns
legend_frameon	true / false	False		Draw a frame around the legend
legend_fontsize	number	computed	pt	Legend font size (default tick_label_size)
labels_title	text	auto		Panel title
labels_xlabel	text	computed		x-axis title (default: category_col)
labels_ylabel	text	Value		y-axis title
title_size	number	12	pt	Panel title font size
title_weight	text	bold		Panel title weight (matplotlib: bold, normal, ...)
axes_label_size	number	10	pt	Axis title font size
axes_label_weight	text	bold		Axis title weight (matplotlib: bold, normal, ...)
tick_label_size	number	8	pt	Tick label font size

binary_motif_heatmap

fig_atlas_omics.renderers:render_binary_motif_heatmap

Key	Type	Default	Unit	What it does
title_size	number	style typography.title_size (else 13)	pt	Panel title font size — lower if the title wraps or crowds the panel
axes_label_size	number	style typography.axes_label_size (else 12.0)	pt	Axis title (x/y label) font size — lower if axis titles clip or crowd
tick_label_size	number	style typography.tick_label_size (else 8)	pt	Tick label font size — lower if tick labels overlap
legend_fontsize	number	style typography.legend_fontsize (else CODE_DEFAULT)	pt	Legend text font size — lower if the legend covers data
orientation	one of vertical, horizontal	vertical		'vertical': genes as rows; 'horizontal': genes as columns, motifs as rows
row_col	text	gene		Column of df with the gene names
tier_col	text	tier		Column of df with each gene's tier
cols	list	auto		Presence columns to show, in order (default: every has_* column)
col_rename_map	mapping	{}		Display label per presence column
col_strip_prefix	text	auto		Prefix removed from presence column names for display (e.g. 'has_')
row_order	list	auto		Gene order (default: order of first appearance)
tier_order	list	auto		Tier order in the stripe and legend
present_color	colour	#2b7bba	hex color	Fill of cells where the motif is present
absent_color	colour	#ffffff	hex color	Fill of cells where it is absent
cell_border_color	colour	#999999	hex color	Cell border colour
cell_border_width	number	0.7	pt	Cell border width
cell_marks	object	auto		Boolean matrix (genes x cols): a dot on those cells (set by the script)
cell_mark_color	colour	white	color	Colour of the cell-mark dots
cell_mark_edgecolor	colour	none	color	Outline of the cell-mark dots
cell_mark_size	number	4.0	pt^2 (marker area)	Size of the cell-mark dots
cell_mark_label	text	auto		Legend text for the cell marks (none = no legend entry)
cell_mark_legend_xy	list	[1.02, -0.12]	axes fraction (x, y)	Position of the cell-mark legend entry
cell_mark_legend_scale	number	8.0	x cell_mark_size	Size of the legend dot relative to the cell dots
tier_colors	mapping	{}	hex color per tier	Colour per tier in the stripe
tier_label_map	mapping	{}		Legend label per tier
tier_bar_label	text	Tier		Label of the tier stripe
stripe_ratio	number	computed	fraction of matrix size	Tier stripe thickness (default 0.024/0.72)
show_tier_legend	true / false	True		Show the tier legend
tier_legend_title	text	Tier		Tier legend title
tier_legend_bbox	list	(1.08, 0.64)	axes fraction (x, y)	Anchor of the tier legend
tier_legend_frameon	true / false	True		Frame around the tier legend
show_binary_legend	true / false	True		Show the present / absent legend
binary_legend_bbox	list	[1.08, 0.72, 0.025, 0.26]	figure fraction [x, y, w, h]	Box of the present / absent legend
present_label	text	present		Legend text for present
absent_label	text	absent		Legend text for absent
labels_title	text	C. Headline Motif Presence (Tier1+2+top Tier3, n=39)		Panel title
title_pad	number	10	pt	Gap between title and matrix
labels_xlabel	text	``		x-axis title
labels_ylabel	text	``		y-axis title
xlabel_pad	number	10	pt	Gap between x tick labels and the x-axis title
ylabel_pad	number	computed	pt	Gap before the y-axis title (default 10, or 40 when horizontal)
ylabel_position	one of left, right	left		Side of the y-axis title
xtick_rotation	number	90	degrees	Column label rotation
xtick_ha	one of left, center, right	center		Horizontal alignment of column labels
row_label_wrap_width	integer	28	characters	Wrap row labels at this width
gene_label_fontsize	number	computed	pt	Gene label size (horizontal; default tick_label_size)
gene_label_rotation	number	90	degrees	Gene label rotation (horizontal)
row_bar_values	list	auto		One summary value per motif row, drawn as a bar right of the matrix
row_bar_labels	list	auto		Text at each bar (default: the value)
row_bar_title	text	auto		Title above the summary bars
row_bar_title_pad	number	3	pt	Gap between the bars and their title
row_bar_gap	number	0.02	figure fraction	Gap between matrix and summary bars
row_bar_width	number	0.2	figure fraction	Width of the summary bar area
row_bar_height	number	0.62	row units	Bar thickness
row_bar_color	colour	#64748b	hex color	Summary bar colour
row_bar_max	number	computed	value units	Bar axis maximum (default: largest value)
row_bar_fontsize	number	computed	pt	Bar label size (default tick_label_size)
gs_left	number	0.08	[0-1] figure fraction	Left edge of the grid
gs_right	number	computed	[0-1] figure fraction	Right edge of the grid (0.80 vertical / 0.86 horizontal)
gs_top	number	computed	[0-1] figure fraction	Top edge of the grid (0.90 vertical / 0.94 horizontal)
gs_bottom	number	computed	[0-1] figure fraction	Bottom edge of the grid (0.25 vertical / 0.15 horizontal)
gs_space	number	computed	fraction of the grid	Gap between tier stripe and matrix

boxplot

fig_atlas.renderers:render_boxplot

Key	Type	Default	Unit	What it does
x_col	text	Sample		Column of df with the groups (x axis)
y_col	text	Expression		Column of df with the values (y axis)
palette	text	Set2		Seaborn palette for the boxes
y_min	number	auto	data units	Lower y limit (both y_min and y_max needed)
y_max	number	auto	data units	Upper y limit
labels_title	text	auto		Panel title (none = no title)
labels_xlabel	text	computed		x-axis title (default: x_col)
labels_ylabel	text	computed		y-axis title (default: y_col)
title_size	number	10	pt	Panel title font size
axes_label_size	number	8	pt	Axis title font size
show_xticklabels	true / false	True		Show x tick labels
show_yticklabels	true / false	True		Show y tick labels
show_legend	true / false	False		Show a legend of the groups

chromosome_ideogram

fig_atlas_omics.renderers:render_chromosome_ideogram

Key	Type	Default	Unit	What it does
start_col	text	start		Column with the band start (bp, 1-based)
end_col	text	end		Column with the band end (bp)
band_col	text	band		Column with the band name
stain_col	text	gie_stain		Column with the Giemsa stain class
marker_pos_col	text	pos		Marker table: column with the position (bp)
marker_label_col	text	label		Marker table: column with the marker text (none: no text)
x_min	number	auto	bp	Left end of a zoomed window (both x_min and x_max; none: whole chromosome)
x_max	number	auto	bp	Right end of a zoomed window
stain_colors	mapping	computed	hex color	Fill per stain class (default: grey scale from white gneg to near-black gpos100; module STAINS)
body_y	number	0.4	axes data units (0-1)	Height of the chromosome centre
body_height	number	0.3	axes data units (0-1)	Chromosome thickness
rounded	true / false	True		Round the chromosome ends (whole-chromosome view)
round_frac	number	0.012	fraction of the chromosome length	Radius of the rounded ends — raise for rounder ends
outline_color	colour	#1f2937	hex color	Outline colour
outline_width	number	0.5	pt	Outline width
show_band_labels	true / false	True		Write band names
band_label_size	number	5.0	pt	Band name size
band_label_rotation	number	90.0	degrees	Band name rotation
band_label_pad	number	0.03	axes data units	Gap between body and band names
band_label_position	one of above, inside	above		Band names above the body, or centred inside it (zoomed strip)
band_label_color	colour	#111827	hex color	Band name colour (above the body)
band_label_inside_color	colour	#ffffff	hex color	Band name colour inside a dark band (inside position)
dark_stains	list	['gpos66', 'gpos75', 'gpos100']		Stains on which inside text uses band_label_inside_color
band_label_clear_frac	number	0.0	fraction of the shown width	Band names centred this close to a marker are left out (0: keep all) — raise if a marker arrow covers a band name
band_label_min_frac	number	0.0	fraction of the shown width	Bands narrower than this get no name — raise if names collide
show_ruler	true / false	False		Draw a position axis (zoomed view)
ruler_position	one of top, bottom	top		Side of the position axis
ruler_unit_bp	number	1000000.0	bp per tick unit	Tick unit (1e6: Mb, 1e3: kb)
ruler_suffix	text	Mb		Text after each tick value
ruler_decimals	integer	2	digits	Decimals in tick values
ruler_nbins	integer	5	ticks	Approximate number of ruler ticks
marker_color	colour	#111827	hex color	Marker arrow and text colour
marker_style	one of arrow, line	arrow		Arrow from above, or a vertical line through the body
marker_length	number	0.25	axes data units	Length of a marker arrow
marker_width	number	1.0	pt	Marker line width
marker_head	number	6.0	pt	Marker arrow head size (head is 0.4 x this long)
marker_label_size	number	6.0	pt	Marker text size
labels_title	text	auto		Name under the chromosome, e.g. 'Chromosome 2' (none: no name)
title_size	number	style typography.title_size (else 8.0)	pt	Panel title font size — lower if the title wraps or crowds the panel
tick_label_size	number	auto	pt	Ruler tick label size (default: rcParams)
title_y	number	0.0	axes data units (0-1)	Height of the name's top edge
text_color	colour	#111827	hex color	Colour of the name

cis_linkage_panel

fig_atlas_omics.renderers:render_cis_linkage_panel

Key	Type	Default	Unit	What it does
wspace	number	0.35	fraction of the mean panel width	Gap between the decay bars and the scatter — raise if the scatter's y label touches the bars
distance_bins	list	['<2kb', '2-10kb', '10-50kb', '50-100kb']		Distance bins, in order
bar_colors	list	['#991B1B', '#E11D48', '#F87171', '#CBD5E1']	hex colors	One colour per distance bin
decay_title	text	Spatial Distance Decay		Title of the decay bar panel
bar_label_size	number	8.5	pt	Count label size on the bars
scatter_title	text	computed		Title of the scatter (default shows the pair count)
r_threshold	number	0.5	Pearson r	Significance line; pairs above it are highlighted
bg_color	colour	#94A3B8	hex color	Colour of pairs below the threshold
bg_size	number	13	pt^2 (marker area)	Marker size of pairs below the threshold
bg_alpha	number	0.28	alpha [0-1]	Opacity of pairs below the threshold
sig_color	colour	#E11D48	hex color	Colour of pairs above the threshold and of the threshold line
sig_edge	colour	#881337	hex color	Outline of pairs above the threshold
sig_size	number	28	pt^2 (marker area)	Marker size of pairs above the threshold
sig_alpha	number	0.85	alpha [0-1]	Opacity of pairs above the threshold
callouts	list	[('FOSB', 5.5, 0.993, (20, 0.94)), ('TUBB4B', 0.5, 0.964, (20, 0.81)), ('IDH2', 1.0, 0.964, (20, 0.68)), ('PDCD10', 0.5, 0.939, (20, 0.55))]	data coords	Labelled genes: [gene, x, y, [text_x, text_y]] each
callout_size	number	8.5	pt	Callout label size
badge_size	number	8.5	pt	Size of the summary badge text
legend_size	number	9.0	pt	Legend font size
title_size	number	13.0	pt	Panel title font size
axes_label_size	number	11.5	pt	Axis title font size

clustered_go_heatmap

fig_atlas_omics.renderers:render_clustered_go_heatmap

Key	Type	Default	Unit	What it does
cmap	colormap	RdBu_r		Diverging colormap for the signed scores
vmax	number	10.0	value units (signed -log10 FDR)	Colour scale runs -vmax..+vmax — lower to stretch contrast for weak clusters
cell_sig_thresh	number	1.3	|value| (1.3 = FDR 0.05)	Cells at or above it print their value; below it a placeholder dash
cell_text_color_mode	one of threshold, contrast	threshold		'threshold': white text above cell_contrast_thresh; 'contrast': by contrast with the cell colour
cell_contrast_thresh	number	5.5	|value|	Above it cell text is white (threshold mode) — lower if mid-dark cells have hard-to-read black text
cell_fontsize	number	9.2	pt	Cell value font size
cell_fontweight	text	bold		Cell value font weight
placeholder_color	colour	#94A3B8	hex color	Colour of the dash in non-significant cells
ytick_fontsize	number	9.8	pt	Row (cluster) label size
ytick_fontweight	text	bold		Row label font weight
species_tick_labels	list	['● Human', '◆ Mouse']		Tick labels of the two species columns per condition
c_human	colour	#2563EB	hex color	Colour of the human tick labels
c_mouse	colour	#DC2626	hex color	Colour of the mouse tick labels
xtick_fontsize	number	11.0	pt	Species tick label size
xtick_rotation	number	45.0	degrees	Species tick label rotation
cond_label_fontsize	number	11.5	pt	Condition label size
cond_label_y	number	-0.58	data coords (rows)	Vertical position of the condition labels — lower (more negative) moves them further below the species ticks
divider_color	colour	#1E293B	hex color	Line between conditions
divider_lw	number	1.4	pt	Width of the line between conditions
species_divider_color	colour	#CBD5E1	hex color	Line between the two species of a condition
species_divider_lw	number	0.7	pt	Width of the species divider

count_summary

fig_atlas_omics.renderers:render_count_summary

Key	Type	Default	Unit	What it does
fdr_max	number	0.05	FDR	Only rows with FDR at or below this are counted
lfc_min	number	0.585	|log2FC|	Only rows with |log2FC| at or above this are counted
as_pct	true / false	False		Show each dataset's counts as a percentage of its rows
unit	text	genes		Noun used in the default axis title and title
order	list	auto		Dataset order, left to right (default: order in the data)
label_rename_map	mapping	{}		Display label per dataset
up_color	colour	#c0392b	hex color	Colour of the up bars (above zero)
down_color	colour	#2c6fbb	hex color	Colour of the down bars (below zero)
zero_line_color	colour	#333333	hex color	Zero line colour
zero_line_width	number	0.8	pt	Zero line width
show_value_labels	true / false	True		Print the count on each bar
value_label_fontsize	number	computed	pt	Count label size (default tick_label_size)
show_legend	true / false	True		Show the up/down legend
legend_loc	text	upper right		Legend location (matplotlib loc string)
labels_title	text	computed		Panel title (default names the cutoffs)
labels_ylabel	text	computed		y-axis title (default 'Number of ' or '% of ')
xtick_rotation	number	30	degrees	Dataset label rotation
title_size	number	13	pt	Panel title font size
axes_label_size	number	11	pt	Axis title font size
tick_label_size	number	8	pt	Tick label font size

cross_condition_dotplot

fig_atlas_omics.renderers:render_cross_condition_dotplot

Key	Type	Default	Unit	What it does
title_size	number	style typography.title_size (else 13)	pt	Panel title font size — lower if the title wraps or crowds the panel
axes_label_size	number	style typography.axes_label_size (else 11)	pt	Axis title (x/y label) font size — lower if axis titles clip or crowd
tick_label_size	number	style typography.tick_label_size (else 8)	pt	Tick label font size — lower if tick labels overlap
term_col	text	GO Term		Column of df with the term (row) names
condition_col	text	Condition		Column of df with the condition (column) names
value_col	text	Signed -log10(FDR)		Column of df with the value mapped to colour
size_col	text	Gene Ratio		Column of df with the value mapped to dot size
direction_col	text	Direction		Column of df with UP/DOWN, used by top_n_up / top_n_down
term_strip_pattern	text	auto		Regex removed from term names before display
condition_order	list	auto		Column order (default: order of first appearance)
condition_rename_map	mapping	{}		x-tick label per raw condition (matching uses raw names)
term_order	list	auto		Row order (default: order of first appearance)
top_n_up	integer	auto	terms	Keep only the top N UP terms per condition
top_n_down	integer	auto	terms	Keep only the top N DOWN terms per condition
cmap	colormap	RdBu_r		Colormap for value_col
color_auto	true / false	True		Colour range symmetric around 0 from the data (else color_min / color_max)
color_min	number	-10.0	value units	Lower end of the colour range when color_auto is false
color_max	number	10.0	value units	Upper end of the colour range when color_auto is false
gray_threshold	number	auto	value units	Values below it are drawn in gray_color and the colour scale starts there (e.g. -log10 0.05)
gray_color	colour	#d0d0d0	hex color	Fill of dots below gray_threshold ('#ffffff' for hollow, ring-only dots)
dot_size_min	number	20.0	pt^2 (marker area)	Area of the smallest dot — raise if small dots vanish
dot_size_scale	number	800.0	pt^2 per unit of size_col	Dot area added per unit of size_col — lower if dots overlap their neighbours
dot_edgecolor	colour	#555555	hex color	Dot outline colour
dot_edgewidth	number	0.5	pt	Dot outline width
dot_alpha	number	0.9	[0-1] opacity	Dot opacity
grid	true / false	True		Draw the background grid
labels_title	text	Cross-Condition GO Dot Plot		Panel title
term_label_side	one of left, right	right		Side the term labels sit on
term_fontsize	number	computed	pt	Term label font size (default tick_label_size)
ylabel_wrap_width	integer	40	characters	Wrap term labels at this width
xtick_fontsize	number	computed	pt	Condition label font size (default tick_label_size)
xtick_rotation	number	45	degrees	Condition label rotation
xtick_ha	one of left, center, right	right		Horizontal alignment of rotated condition labels
xtick_rotation_mode	text	auto		'anchor' keeps multi-line rotated labels aligned (matplotlib rotation_mode)
reposition_axes	true / false	True		Shrink the axes to make room for term labels and the colorbar
label_margin_pad	number	1.2	x measured label width	Room reserved for term labels beyond their measured width — raise to shrink the plot area further
label_margin_cap	number	0.82	[0-1] panel fraction	Most of the panel the labels may claim
min_plot_frac	number	0.22	[0-1] panel fraction	Least of the panel kept for the dots
show_colorbar	true / false	True		Show the colourbar
cax	object	auto		An existing axes to draw the colourbar in (set by the script, not in YAML)
colorbar_loc	text	computed		Side of the colourbar (matplotlib location)
colorbar_orientation	one of vertical, horizontal	vertical		Colourbar orientation when cax is given
colorbar_shrink	number	0.6	fraction of axes height	Length of the side colourbar
colorbar_margin	number	computed	[0-1] panel fraction	Side margin reserved for the colourbar (default 0.14, or 0.03 without one)
colorbar_top_right	true / false	False		Small horizontal colourbar above the top-right corner instead of a side bar
colorbar_width_in	number	3.0	inches	Width of the top-right colourbar
colorbar_height_in	number	0.16	inches	Height of the top-right colourbar
colorbar_gap_in	number	0.25	inches	Gap between panel top and the top-right colourbar
colorbar_right_pad_in	number	0.1	inches	Inset of the top-right colourbar from the right edge
colorbar_label	text	sign(dir) x -log10(FDR)		Colourbar title
colorbar_label_fontsize	number	computed	pt	Colourbar title size (default from axes_label_size)
colorbar_tick_fontsize	number	computed	pt	Colourbar tick size (default from tick_label_size)
show_size_legend	true / false	True		Show the dot-size legend
size_legend_title	text	Gene Ratio		Dot-size legend title
size_legend_values	list	auto	size_col units	Sizes shown in the legend (default: from the data)
size_legend_loc	text	best		Legend anchor inside the axes (matplotlib loc)
size_legend_outside	true / false	False		Place the legend outside, left of the dots, anchored at size_legend_bbox
size_legend_bbox	list	(0.0, 0.02)	axes fraction (x, y)	Anchor of the outside legend
size_legend_offset_pts	number	-62	pt	Horizontal shift of the outside legend — more negative moves it further left of the dots
size_legend_below	true / false	False		Place the legend centred below the axes
size_legend_below_offset_pts	number	30	pt	Gap between the axes and the legend below it
size_legend_ncol	integer	computed	columns	Columns of the legend below (default: all sizes in one row)

cross_condition_heatmap

fig_atlas_omics.renderers:render_cross_condition_heatmap

Key	Type	Default	Unit	What it does
title_size	number	style typography.title_size (else 13)	pt	Panel title font size — lower if the title wraps or crowds the panel
tick_label_size	number	style typography.tick_label_size (else 8)	pt	Tick label font size — lower if tick labels overlap
term_col	text	GO Term		Column of df with the term (row) names
condition_col	text	Condition		Column of df with the condition (column) names
value_col	text	Signed -log10(FDR)		Column of df with the signed enrichment value
term_strip_pattern	text	auto		Regex removed from term names before display (e.g. a GO ID prefix)
condition_order	list	auto		Column order (default: order of first appearance)
condition_rename_map	mapping	{}		Display label per condition — raw name -> label
column_groups	list	auto		Column group banners over the matrix, one item per group: label, start / end (column index), color, y_banner (1.04) and line_y (1.02) in axes fraction, line_width (2.2 pt)
cluster_rows	true / false	True		Order rows by hierarchical clustering (needs > 2 rows)
metric	text	euclidean		Row distance for clustering (scipy pdist metric)
linkage	text	average		Linkage method for row clustering (scipy)
show_cluster_bands	true / false	False		Split rows into clusters with a labelled header row each
cluster_dist_threshold	number	auto	dendrogram distance	Cut height for the cluster bands (default: cluster_dist_threshold_frac x the tallest merge)
cluster_dist_threshold_frac	number	0.7	fraction of the tallest merge	Relative cut height when cluster_dist_threshold is unset — lower for more, smaller bands
cluster_band_color	colour	#4F46E5	hex color	Colour of the cluster band headers
colors	mapping	{}	hex color per bin	Colour of each bin: up3/up2/up1/absent/down1/down2/down3 (FDR < 0.001 / 0.01 / 0.05)
bin_edges	list	[2.0, 3.0]	-log10 FDR	Edges between the 3 strength bins (default 2 and 3 = FDR 0.01 and 0.001)
show_cell_borders	true / false	True		Draw a grid between cells
cell_border_color	colour	lightgrey	color	Cell grid colour
cell_border_width	number	0.5	pt	Cell grid line width
split_vline	number	auto	column index (data coords)	Dashed vertical divider at this x (e.g. 3.5 between human and mouse columns)
split_vline_color	colour	#333333	hex color	Divider colour
split_vline_style	text	--		Divider line style (matplotlib)
split_vline_width	number	1.8	pt	Divider width
labels_title	text	Cross-Condition GO Heatmap		Panel title
title_pad	number	computed	pt	Gap between title and matrix (default 24 with column banners, else 6) — raise if banners touch the title
group_banner_fontsize	number	computed	pt	Column banner font size (default title_size - 1.5)
show_term_labels	true / false	True		Show the term (row) labels
term_fontsize	number	computed	pt	Term label font size (default tick_label_size)
term_label_wrap_width	integer	28	characters	Wrap term labels at this width — raise for fewer, longer lines
xtick_rotation	number	45	degrees	Condition label rotation
show_legend	true / false	True		Show the bin legend
legend_loc	text	upper right		Legend anchor (matplotlib loc, figure coords)
gs_left	number	0.03	[0-1] figure fraction	Left edge of the plot grid
gs_right	number	0.98	[0-1] figure fraction	Right edge of the plot grid
gs_top	number	0.88	[0-1] figure fraction	Top edge of the plot grid — lower if the title clips
gs_bottom	number	0.12	[0-1] figure fraction	Bottom edge of the plot grid — raise if rotated condition labels clip
dendro_width	number	0.12	fraction of the grid width	Width of the row dendrogram
dendro_wspace	number	0.02	fraction of the grid width	Gap between dendrogram and matrix
label_margin_pad	number	1.2	x label width	Room reserved for term labels relative to their width — raise if term labels clip at the left
label_margin_cap	number	0.72	[0-1] grid fraction	Upper limit on the room reserved for term labels

dose_response

fig_atlas.renderers:render_dose_response

Key	Type	Default	Unit	What it does
group_col	text	auto		Column splitting the data into coloured groups (default: one group)
group_order	list	auto		Group order in drawing and legend (default: order in the data)
group_colors	mapping	{}	hex color	Colour per group (default: matplotlib colour cycle)
group_labels	mapping	{}		Legend label per group (default: the group value)
color	colour	#4b5563	hex color	Colour when there is no group_col
x_log	true / false	True		Log-scaled dose axis (the usual way to show a dose series)
x_min	number	auto	data coords	Lower x limit (both x_min and x_max needed)
x_max	number	auto	data coords	Upper x limit
y_log	true / false	False		Log-scaled y axis
y_min	number	auto	data coords	Lower y limit (both y_min and y_max needed)
y_max	number	auto	data coords	Upper y limit
grid	true / false	False		Draw horizontal grid lines
grid_alpha	number	0.3	[0-1] opacity	Grid opacity
spine_width	number	auto	pt	Axis line width (default: rcParams)
hide_top_right	true / false	True		Hide the top and right axis lines
labels_title	text	auto		Panel title (none: no title)
labels_xlabel	text	computed		x-axis title (default: the x column's name)
labels_ylabel	text	computed		y-axis title (default: the y column's name)
title_size	number	8.0	pt	Panel title size
axes_label_size	number	auto	pt	Axis title size (default: rcParams)
tick_label_size	number	auto	pt	Tick label size (default: rcParams)
show_legend	true / false	True		Show the group legend (only with a group_col)
legend_loc	text	best		Legend location (matplotlib loc)
legend_fontsize	number	auto	pt	Legend font size (none: tick_label_size)
legend_frameon	true / false	False		Draw a frame around the legend
x_col	text	dose		Column with the doses (positive numbers)
y_col	text	response		Column with the responses (one row per replicate)
points	one of mean, all	mean		Per dose: the mean with an error bar, or every replicate
error	one of sem, sd	sem		Error bar of the mean: standard error or standard deviation
marker_size	number	4.0	pt	Point size
capsize	number	2.0	pt	Width of the error-bar caps
error_width	number	0.8	pt	Error-bar line width
fit	true / false	True		Draw the four-parameter logistic fit
fit_line_width	number	1.2	pt	Fit curve width
fit_points	integer	200	points along the dose range	Smoothness of the fit curve
show_ec50	true / false	False		Mark each fitted EC50 with a dashed vertical line
ec50_line_width	number	0.6	pt	EC50 line width

dot_matrix

fig_atlas.renderers:render_dot_matrix

Key	Type	Default	Unit	What it does
row_col	text	row		Column with the row names
col_col	text	column		Column with the column names
size_col	text	auto		Column with the count that sets dot area (absent: one size)
color_col	text	auto		Column with the category that sets dot colour (absent: one colour)
row_group_col	text	auto		Column grouping rows into blocks with a line between them
row_order	list	auto		Row order, top to bottom (default: order in the data)
col_order	list	auto		Column order, left to right (default: order in the data)
col_labels	mapping	{}		Shown name per column
multi	one of first, split	first		A cell with several categories: one dot coloured by the first in color_order, or one dot per category
split_offset	number	0.22	column units	Distance between the dots of a split cell — raise if they touch
color_order	list	auto		Category priority and legend order (default: order in the data)
color_map	mapping	{}	hex color	Colour per category
color_labels	mapping	{}		Legend text per category
default_color	colour	#4b5563	hex color	Dot colour without a category
size_per_unit	number	12.0	pt^2 per count	Dot area per count
size_min	number	10.0	pt^2	Smallest dot area
size_max	number	120.0	pt^2	Largest dot area — lower if dots touch
edge_color	colour	#ffffff	hex color	Dot outline colour
edge_width	number	0.4	pt	Dot outline width
show_counts	true / false	False		Write the count beside each dot
count_size	number	5.0	pt	Size of those counts
count_offset	number	0.28	column units	Horizontal offset of the counts from the dot centre
grid	true / false	True		Draw faint lines through the cells
grid_color	colour	#e5e7eb	hex color	Grid line colour
grid_width	number	0.4	pt	Grid line width
group_line_color	colour	#9ca3af	hex color	Line between row groups
group_line_width	number	0.6	pt	Width of that line
row_label_style	text	normal		Font style of the row names (italic for genes)
tick_length	number	0.0	pt	Tick mark length (0: names only)
x_tick_rotation	number	0.0	degrees	Rotation of the column names
show_legend	true / false	True		Show the colour and size legends
legend_anchor	list	[1.02, 1.0]	axes fraction [x, y]	Upper-left corner of the legend
legend_edge_width	number	0.0	pt	Outline width of the legend dots
size_legend_counts	list	[1, 5]		Counts shown in the size legend (empty: none)
size_legend_label	text	{n}		Text of each size legend entry ({n}: the count)
labels_title	text	auto		Panel title
labels_xlabel	text	auto		x-axis title
labels_ylabel	text	auto		y-axis title
title_size	number	style typography.title_size (else 8.0)	pt	Panel title font size — lower if the title wraps or crowds the panel
axes_label_size	number	auto	pt	Axis title size (default: rcParams)
tick_label_size	number	auto	pt	Row and column name size (default: rcParams)
legend_fontsize	number	auto	pt	Legend text size (default: rcParams)

effect_dots

fig_atlas.renderers:render_effect_dots

Key	Type	Default	Unit	What it does
item_col	text	item		Column with the row names (what each estimate is about)
series_col	text	series		Column with the series (e.g. unadjusted / adjusted; absent: one)
estimate_col	text	estimate		Column with the estimate (dot)
low_col	text	ci_low		Column with the lower confidence limit
high_col	text	ci_high		Column with the upper confidence limit
item_order	list	auto		Row order, top to bottom (default: order in the data)
item_sort	one of data, estimate_desc, estimate_asc	data		Row order when item_order is unset: as in the data, or by the (first series') estimate, largest on top (estimate_desc) or smallest on top
item_labels	mapping	{}		Display label per item
series_order	list	auto		Series order (default: order in the data)
series_colors	mapping	{}		Colour per series
series_labels	mapping	{}		Legend label per series
dodge	number	0.18	row units	Vertical offset between series within a row — raise if the series' intervals overlap
color_by	one of series, threshold	series		Colour each series (series_colors), or each estimate by direction and significance (threshold)
sig_col	text	auto		threshold: column with the significance value (smaller = stronger, e.g. padj)
sig_threshold	number	0.05	significance units	threshold: estimates with sig_col at or below this are up / down
up_color	colour	#D55E00	hex color	threshold: colour of significant positive estimates
down_color	colour	#0072B2	hex color	threshold: colour of significant negative estimates
ns_color	colour	#9CA3AF	hex color	threshold: colour of the others
class_labels	mapping	{'up': 'Up', 'down': 'Down', 'ns': 'n.s.'}		threshold: legend label per class (keys up, down, ns)
marker_size	number	16	pt^2 (marker area)	Point estimate marker size
ci_width	number	0.8	pt	Confidence interval line width
zero_line	true / false	True		Draw the no-effect line at x = 0
zero_line_color	colour	#6b7280	hex color	No-effect line colour
zero_line_width	number	0.5	pt	No-effect line width
zero_line_style	text	-	matplotlib line style	No-effect line style ('-', '--', ':')
xlim	list	auto	data coords [min, max]	x-axis range (default: data)
spine_width	number	0.6	pt	Axis spine width
legend	true / false	True		Show the series legend
legend_loc	text	lower right		Legend location (matplotlib loc string)
legend_anchor	list	auto	axes fraction (x, y)	bbox_to_anchor for the legend
legend_ncol	integer	1	columns	Legend columns
legend_fontsize	number	5.0	pt	Legend font size
title	text	auto		Panel title
xlabel	text	auto		x-axis title
title_pad	number	3.0	pt	Gap between title and axes
title_size	number	6.5	pt	Panel title font size
axes_label_size	number	6.0	pt	Axis title font size
tick_label_size	number	5.5	pt	Tick and row label font size

flow_diagram

fig_atlas.renderers:render_flow_diagram

Key	Type	Default	Unit	What it does
id_col	text	id		Column with each node's unique name (edges refer to it)
x_col	text	x		Column with the node's left edge (diagram units)
y_col	text	y		Column with the node's top edge (diagram units)
w_col	text	w		Column with the node's width
h_col	text	h		Column with the node's height
title_col	text	title		Column with the node's bold first line
body_col	text	body		Column with further lines, separated by newlines
kind_col	text	kind		Column with the node kind: box, group, text, decision or terminal
fill_col	text	fill		Column with a node's own fill colour (empty: box_fill)
color_col	text	color		Column with a node's own text colour (empty: text_color, body_color)
edges	list	[]		Arrows: list of {from, to, label?, from_side?, to_side?, rad?, style?, route?}
xlim	list	auto	diagram units [min, max]	Horizontal extent (default: the nodes)
ylim	list	auto	diagram units [min, max]	Vertical extent (default: the nodes)
y_down	true / false	True		y grows downward, like a page (false: upward, like a plot)
units_per_mm	number	1.0	diagram units per mm	Scale of the diagram units, used to place body text below a title — 1 when the diagram is laid out in mm
box_fill	colour	#F3F4F6	hex color	Box fill
box_edge	colour	#4B5563	hex color	Box outline
box_linewidth	number	0.6	pt	Box outline width
box_radius	number	1.0	diagram units	Corner radius of boxes and groups — 0 for square corners
group_edge	colour	#9CA3AF	hex color	Group outline
group_fill	colour	none	hex color or none	Group fill
group_linestyle	text	--		Group outline style (matplotlib linestyle)
group_linewidth	number	0.6	pt	Group outline width
title_size	number	7.0	pt	Node title size
body_size	number	6.0	pt	Node body size
title_weight	text	bold		Node title weight
text_color	colour	#111827	hex color	Title colour
body_color	colour	#374151	hex color	Body colour
text_align	text	center		Text alignment in boxes: center or left
text_valign	text	center		Vertical placement of a box's or text node's text: center or top — top fills a box from its top edge (text_pad below it); groups always label their top-left corner
text_pad	number	1.5	diagram units	Gap between a box's edge and its text — raise if text touches the outline
line_spacing	number	1.25	multiple of the font size	Line spacing of the body text
title_gap	number	0.8	diagram units	Gap between a node's title and its body
arrow_color	colour	#374151	hex color	Arrow colour
arrow_width	number	0.8	pt	Arrow line width
arrow_head	number	6.0	pt	Arrow head size
arrow_gap	number	0.6	pt	Gap between an arrow's ends and the boxes
dashed_style	list	[0, [3, 2]]	matplotlib dash pattern (offset, [on, off] in pt)	Line style of edges marked style: dashed
route	one of straight, elbow	straight		How edges run: straight lines, or right-angle segments as in flowcharts (an edge's own route wins)
elbow_offset	number	4.0	diagram units	How far a U-shaped elbow edge (two sides facing the same way) runs out past the nodes — raise if the return line crowds the boxes it passes
level_edges	true / false	True		Draw a straight arrow level (horizontal or vertical) when the two nodes' spans overlap — false to join the middles of the two sides, even if the arrow then slants
edge_label_size	number	6.0	pt	Edge label size
edge_label_color	colour	#374151	hex color	Edge label colour
edge_label_offset	number	1.2	diagram units	Edge label distance from the arrow's middle (above a horizontal arrow, right of others)

funnel

fig_atlas.renderers:render_funnel

Key	Type	Default	Unit	What it does
bar_color	colour	#3b73b9	hex color	Fill colour of the funnel bars
bar_edgecolor	colour	black	color	Bar outline colour
bar_width	number	0.5	fraction of the category spacing	Bar width — lower to separate the steps more
show_value_labels	true / false	True		Print the count on each bar
value_position	one of top, inside	top		Count above the bar ('top') or centred inside it
value_color	colour	black	color	Count label colour
value_fontsize	number	computed	pt	Count label size (default axes_label_size)
labels_title	text	Target narrowing		Panel title
labels_subtitle	text	auto		Second line under the title
labels_ylabel	text	count		y-axis title
title_pad	number	12.0	pt	Gap between title and axes — raise if the title touches the value labels
xtick_rotation	number	0	degrees	Step label rotation (non-zero labels are right-aligned)
title_size	number	13	pt	Panel title font size
subtitle_size	number	9	pt	Subtitle font size
axes_label_size	number	11	pt	Axis title font size
tick_label_size	number	8	pt	Tick label font size

gene_model_track

fig_atlas_omics.renderers:render_gene_model_track

Key	Type	Default	Unit	What it does
gene_col	text	gene_name		Column with the gene name
transcript_col	text	transcript_id		Column with the transcript id
strand_col	text	strand		Column with + / -
exon_start_col	text	exon_start		Column with the exon start (bp, 1-based)
exon_end_col	text	exon_end		Column with the exon end (bp)
collapse	one of longest, all	longest		One transcript per gene (the longest), or all
hide_pattern	text	auto		Regular expression; genes whose name matches are left out (none: keep all) — e.g. '^(ENSMUSG|Gm\d)' hides unnamed and predicted genes
x_min	number	auto	bp	Left end of the window (both x_min and x_max; none: the data extent)
x_max	number	auto	bp	Right end of the window
max_rows	integer	3	rows	Most rows of genes — raise if names are dropped onto busy rows
row_gap_frac	number	0.01	fraction of the window	Smallest gap between two genes (with their names) on one row
gene_color	colour	#1e3a8a	hex color	Colour of exons, introns and chevrons
highlight_colors	mapping	{}	hex color	Colour per gene name to pick out
exon_height	number	0.5	fraction of a row	Exon box height
intron_width	number	0.6	pt	Intron line width
chevron_spacing_frac	number	0.025	fraction of the window	Distance between strand chevrons (0: none) — raise for fewer chevrons
chevron_edge_width	number	0.0	pt	Chevron outline width (0: filled only)
chevron_size	number	2.5	pt	Chevron marker size
show_labels	true / false	True		Write gene names
label_size	number	6.0	pt	Gene name size
label_style	text	italic		Gene name font style
label_position	one of below, left	below		Names under the model, or left of it
label_pad	number	0.08	fraction of a row	Gap between a model and its name
label_char_em	number	0.6	em per character	Estimated text width per character (packing only) — raise if names on one row touch
text_color	colour	#111827	hex color	Gene name colour

go_bar

fig_atlas_omics.renderers:render_go_bar

Key	Type	Default	Unit	What it does
top_n	integer	15	terms	Terms shown after sorting
sort_by	one of FDR (ascending), Gene Count (descending), Alphabetical	FDR (ascending)		Order of the terms
x_axis	one of -log10(FDR), Gene Ratio, Fold Enrichment	-log10(FDR)		Bar length metric
horizontal	true / false	True		Horizontal bars (terms on the y axis)
label_strip_pattern	text	auto		Regex removed from term names (e.g. GO IDs)
ylabel_wrap_width	integer	70	characters	Wrap term names at this width
bar_color	colour	#4C72B0	hex color	Bar fill colour
bar_edgecolor	colour	black	color	Bar outline colour
bar_edgewidth	number	0.5	pt	Bar outline width
show_threshold_line	true / false	False		Draw the FDR cutoff (only with x_axis -log10(FDR))
threshold_fdr	number	0.05	FDR	FDR of the cutoff line
threshold_line_color	colour	black	color	Cutoff line colour
threshold_line_style	text	--		Cutoff line style (matplotlib linestyle)
threshold_line_width	number	1.0	pt	Cutoff line width
threshold_line_alpha	number	0.6	alpha [0-1]	Cutoff line opacity
grid	true / false	True		Draw grid lines along the value axis
grid_style	text	--		Grid line style (matplotlib linestyle)
grid_alpha	number	0.3	alpha [0-1]	Grid line opacity
labels_title	text	GO/KEGG Enrichment Bar Chart		Panel title
xlabel_text	text	computed		Value axis title (default: the x_axis name)
ylabel_text	text	GO/KEGG Terms		Term axis title
xtick_rotation	number	45	degrees	Tick label rotation of the category axis in vertical mode
title_size	number	13	pt	Panel title font size
axes_label_size	number	11	pt	Axis title font size
tick_label_size	number	8	pt	Tick label font size

go_cluster_dot

fig_atlas_omics.renderers:render_go_cluster_dot

Key	Type	Default	Unit	What it does
top_n	integer	20	clusters	Clusters shown
top_n_by	one of FDR, Fold Enrichment	FDR		Which clusters are kept when there are more than top_n
sort_by	one of FDR, Cluster Size, Term Name	FDR		Row order of the kept clusters
ylabel_wrap_width	integer	60	characters	Characters kept from each term name
x_axis	one of -log10(FDR), Gene Ratio, Fold Enrichment	Fold Enrichment		Metric on the x axis
x_min	number	auto	data coords	Lower x limit (default: data)
x_max	number	auto	data coords	Upper x limit (default: data)
y_min	number	auto	row index	Lower y limit (default: data)
y_max	number	auto	row index	Upper y limit (default: data)
show_zero_line	true / false	True		Draw the x = 0 reference line
zero_line_color	colour	gray	color	Reference line colour
zero_line_width	number	0.6	pt	Reference line width
zero_line_style	text	-		Reference line style (matplotlib linestyle)
color_by	one of Fold Enrichment, Fold Enrichment (median), FDR, Ontology, Direction	Fold Enrichment		What the dot colour encodes
cmap	text	computed		Colormap (default YlOrRd for fold enrichment, viridis_r for FDR)
z_auto	true / false	True		Colour scale from the data; set false to use z_min/z_max
z_min	number	computed	colour metric units	Lower colour limit when z_auto is false
z_max	number	computed	colour metric units	Upper colour limit when z_auto is false
direction_colors	mapping	{'UP': '#e74c3c', 'DOWN': '#3498db', 'TOTAL': '#95a5a6'}	hex color	Colour per direction when color_by is Direction
dot_default_color	colour	#3498db	hex color	Dot colour when the color_by column is missing
colorbar_loc	one of right, left, top, bottom	right		Side of the colourbar
colorbar_shrink	number	0.6	fraction of the axes height	Colourbar length
color_legend_loc	text	best		Location of the Ontology/Direction colour key
size_by	one of Cluster size, Gene count	Cluster size		What the dot size encodes
dot_size_min	number	40.0	pt^2 (marker area)	Size of the smallest dot
dot_size_scale	number	20.0	pt^2 per unit	Added area per member or gene — lower if large dots overlap
dot_alpha	number	0.85	alpha [0-1]	Dot opacity
dot_edgecolor	colour	black	color	Dot outline colour
dot_edgewidth	number	0.8	pt	Dot outline width
show_size_legend	true / false	True		Show the dot size legend
size_legend_loc	text	best		Size legend location (matplotlib loc string)
size_legend_values	list	auto		Values shown in the size legend (default: three spread values)
labels_title	text	computed		Panel title (default names top N and the size metric)
title	text	computed		Older name of labels_title, used when labels_title is not set
title_size	number	13	pt	Panel title font size
axes_label_size	number	11	pt	Axis title font size
tick_label_size	number	8	pt	Tick label font size

go_dot

fig_atlas_omics.renderers:render_go_dot

Key	Type	Default	Unit	What it does
top_n	integer	20	terms	Terms shown (highest on the x measure)
x_axis	one of Gene Ratio, Fold Enrichment	Gene Ratio		Measure on the x axis
size_mode	one of Gene Count, Gene Ratio, Fold Enrichment	Gene Count		Measure mapped to dot size
palette	colormap	YlOrRd_r		Colormap for the adjusted P
color_min	number	0.0	adjusted P	Lower end of the colour scale
color_max	number	0.05	adjusted P	Upper end of the colour scale
ylabel_wrap_width	integer	26	characters	Wrap term labels at this width
xlabel_text	text	computed		x-axis title (default: the x_axis name)
title_size	number	13	pt	Panel title font size
axes_label_size	number	11	pt	Axis title font size
tick_label_size	number	8	pt	Tick label font size

go_rrvgo_treemap

fig_atlas_omics.renderers:render_go_rrvgo_treemap

Key	Type	Default	Unit	What it does
size_floor_frac	number	0.03	fraction of the panel's largest term	Smallest cell size, so zero-size terms stay visible as slivers
cmap	text	hue		Cluster colours: a qualitative colormap name, or 'hue' for an even hue sweep
canvas_width	number	100.0	treemap units	Width of the layout canvas (height follows the axes' aspect)
edge_color	colour	black	color	Cell outline colour
edge_width	number	1.0	pt	Cell outline width
cluster_border_color	colour	computed	color	Outline around each cluster (default edge_color)
cluster_border_width	number	computed	pt	Cluster outline width (default 2.5 x edge_width)
label_min_area_frac	number	0.004	fraction of the canvas area	Cells smaller than this get no label — raise if small cells are crowded with text
label_wrap_width	integer	14	characters	Wrap cell labels at this width
hub_label_size	number	11	pt	Cluster (parent term) label size
member_label_size	number	7.5	pt	Member term label size
max_dispensability	number	auto	rrvgo dispensability [0-1]	Drop terms more dispensable than this
labels_title	text	GO rrvgo Cluster Treemap		Panel title
title_size	number	13	pt	Panel title font size

group_scatter

fig_atlas.renderers:render_group_scatter

Key	Type	Default	Unit	What it does
x_col	text	x		Column with the x values
y_col	text	y		Column with the y values
group_col	text	group		Column with the group of each point (absent: one group)
label_col	text	label		Column with the text written beside each point (with point_labels)
group_order	list	auto		Group draw order (default: order in the data)
group_colors	mapping	{}		Point colour per group (unlisted groups are grey)
group_labels	mapping	{}		Legend label per group
marker_size	number	14	pt^2 (marker area)	Point size
edgecolor	colour	white	color	Point outline colour
edgewidth	number	0.4	pt	Point outline width
point_labels	true / false	auto		Write the label column next to each point
point_label_offset	list	[2, 1]	points (dx, dy)	Offset of the point labels
point_label_fontsize	number	4.6	pt	Point label size
fit	true / false	True		Draw a least-squares line over all points
fit_color	colour	#374151	hex color	Fit line colour
fit_width	number	0.7	pt	Fit line width
fit_style	text	-		Fit line style (matplotlib linestyle)
annotate_r	true / false	True		Print the Pearson r and P
r_fmt	text	r = {r:+.2f}, P = {p:.1g}		Format of the r text; fields r, p, n
r_xy	list	[0.03, 0.97]	axes fraction (x, y)	Top-left corner of the r text
r_fontsize	number	5.5	pt	r text size
xlim	list	auto	data coords [min, max]	x-axis range (default: data)
ylim	list	auto	data coords [min, max]	y-axis range (default: data)
zero_line	true / false	True		Draw the y = 0 line
zero_line_color	colour	#9ca3af	hex color	Zero line colour
zero_line_width	number	0.4	pt	Zero line width
spine_width	number	0.6	pt	Axis spine width
legend	true / false	auto		Show the group legend
legend_loc	text	lower right		Legend location (matplotlib loc string)
legend_fontsize	number	5.0	pt	Legend font size
title	text	auto		Panel title
xlabel	text	auto		x-axis title
ylabel	text	auto		y-axis title
title_pad	number	3.0	pt	Gap between title and axes
title_size	number	6.5	pt	Panel title font size
axes_label_size	number	6.0	pt	Axis title font size
tick_label_size	number	5.5	pt	Tick label font size

grouped_hbar

fig_atlas.renderers:render_grouped_hbar

Key	Type	Default	Unit	What it does
title_size	number	style typography.title_size (else 13)	pt	Panel title font size — lower if the title wraps or crowds the panel
axes_label_size	number	style typography.axes_label_size (else 11)	pt	Axis title (x/y label) font size — lower if axis titles clip or crowd
tick_label_size	number	style typography.tick_label_size (else 8)	pt	Tick label font size — lower if tick labels overlap
legend_fontsize	number	style typography.legend_fontsize (else CODE_DEFAULT)	pt	Legend text font size — lower if the legend covers data
category_col	text	category		Column of df holding the row categories (y axis)
series	list	auto		Columns of df drawn as side-by-side bars, in this order (required)
series_labels	mapping	{}		Legend label per series column — map column -> text
series_colors	mapping	{}	hex color per series	Bar colour per series column; unset series cycle indigo / amber / teal
category_order	list	auto		Row order top to bottom; default: order of first appearance
bar_height	number	0.36	data units (row spacing = 1)	Height of each bar; a group of n bars spans n x this — raise for thicker bars, lower for gaps
ylabel_wrap_width	integer	0	characters	Wrap row labels at this width (0 = no wrap) — lower if row labels push the plot right
xlim	list	auto	data coords [min, max]	x-axis range; only the max is used (min is 0) — default: 1.15 x the largest bar
show_value_labels	true / false	True		Print each bar's count at its end
value_label_fontsize	number	computed	pt	Count label size (default: tick label size) — lower if labels overlap the next bar
value_label_offset	number	0.012	fraction of x range	Gap between bar end and its count — raise if labels touch the bars
xlabel	text	count		x-axis title
labels_title	text	``		Panel title (empty = none)
show_legend	true / false	True		Show the series legend
legend_loc	text	lower right		Legend anchor (matplotlib loc) — move it off the bars

heatmap

fig_atlas.renderers:render_heatmap

Key	Type	Default	Unit	What it does
label_col	text	auto		Column with the row labels (default: symbol, else gene_id, else the row number)
sample_columns	list	auto		Columns to show as samples (default: every numeric column that is not a statistic such as padj or log2FC)
n_genes	integer	50	genes	Genes shown (after sorting)
max_gene_labels	integer	20	genes	Genes are named only up to this many rows (more: no names, rather than row numbers) — raise with a taller panel and a smaller tick_label_size
sorting	one of padj, log2fc, clustering	padj		How the genes are chosen and ordered
normalization	one of z-score, minmax, log2, none	z-score		Per-gene scaling of the values
transpose	true / false	False		Samples as rows, genes as columns
sample_rename_map	mapping	{}		Display label per raw sample name
show_dendrogram	true / false	False		Draw the clustering dendrogram
colormap	colormap	RdBu_r		Colormap of the heatmap
colorbar_min	number	auto	value units	Lower end of the colour scale (default: data)
colorbar_max	number	auto	value units	Upper end of the colour scale (default: data)
show_colorbar	true / false	True		Show the colourbar
labels_title	text	auto		Panel title
labels_xlabel	text	auto		x-axis title
labels_ylabel	text	auto		y-axis title
show_xticklabels	true / false	True		Show column labels
show_yticklabels	true / false	True		Show row labels
xtick_label_rotation	number	90	degrees	Column label rotation
xtick_label_alignment	text	computed		Column label alignment (default: center at 0/90 degrees, else right)
title_size	number	10	pt	Panel title font size
axes_label_size	number	8	pt	Axis title font size
tick_label_size	number	6	pt	Tick label font size

histogram

fig_atlas.renderers:render_histogram

Key	Type	Default	Unit	What it does
group_col	text	auto		Column splitting the data into coloured groups (default: one group)
group_order	list	auto		Group order in drawing and legend (default: order in the data)
group_colors	mapping	{}	hex color	Colour per group (default: matplotlib colour cycle)
group_labels	mapping	{}		Legend label per group (default: the group value)
color	colour	#4b5563	hex color	Colour when there is no group_col
x_log	true / false	False		Log-scaled x axis
x_min	number	auto	data coords	Lower x limit (both x_min and x_max needed)
x_max	number	auto	data coords	Upper x limit
y_log	true / false	False		Log-scaled y axis
y_min	number	auto	data coords	Lower y limit (both y_min and y_max needed)
y_max	number	auto	data coords	Upper y limit
grid	true / false	False		Draw horizontal grid lines
grid_alpha	number	0.3	[0-1] opacity	Grid opacity
spine_width	number	auto	pt	Axis line width (default: rcParams)
hide_top_right	true / false	True		Hide the top and right axis lines
labels_title	text	auto		Panel title (none: no title)
labels_xlabel	text	computed		x-axis title (default: the x column's name)
labels_ylabel	text	computed		y-axis title (default: the y column's name)
title_size	number	8.0	pt	Panel title size
axes_label_size	number	auto	pt	Axis title size (default: rcParams)
tick_label_size	number	auto	pt	Tick label size (default: rcParams)
show_legend	true / false	True		Show the group legend (only with a group_col)
legend_loc	text	best		Legend location (matplotlib loc)
legend_fontsize	number	auto	pt	Legend font size (none: tick_label_size)
legend_frameon	true / false	False		Draw a frame around the legend
x_col	text	value		Column with the values
bins	integer	20	number of bins	Number of equal-width bins (shared by all groups) — lower for small samples, raise for large ones
bin_min	number	auto	data coords	Left edge of the first bin (default: smallest value)
bin_max	number	auto	data coords	Right edge of the last bin (default: largest value)
density	true / false	False		Show density (area 1 per group) instead of counts, so groups of different size compare
style	one of step, bar	step		Outlines (step) or filled bars (bar); outlines read better with several groups
line_width	number	1.0	pt	Outline width
fill_alpha	number	0.35	[0-1] opacity	Fill opacity of bars (style bar)

image_panel

fig_atlas.renderers:render_image_panel

Key	Type	Default	Unit	What it does
channel_colors	list	auto	matplotlib colours, one per file	Tint per greyscale channel when several files are combined (default: green, magenta, cyan, ...)
channel_labels	list	auto		Name per channel, shown in a corner when show_channel_labels
display_ranges	list	auto	image units [min, max] per channel	Linear display range per channel (default: from display_percentiles)
display_percentiles	list	[0.0, 100.0]	percentiles [low, high]	Display range taken from the image when display_ranges is not set — e.g. [0.5, 99.5] to ignore a few saturated pixels
gamma	number	1.0	exponent	Gamma on the scaled image; anything but 1 is a nonlinear adjustment and verify warns
crop	list	auto	pixels [x0, y0, x1, y1]	Region shown (default: the whole image)
interpolation	text	nearest		Resampling when drawn (matplotlib imshow; nearest keeps pixels)
panel	text	auto		Panel letter recorded with the adjustments (README 'Images' section)
pixel_size	number	auto	physical units per pixel	Size of one pixel; needed for a scale bar
pixel_unit	text	µm		Unit of pixel_size and scale_bar
scale_bar	number	auto	physical units (pixel_unit)	Scale bar length (default: no bar)
scale_bar_position	one of lower right, lower left, upper right, upper left	lower right		Corner of the scale bar
scale_bar_color	colour	white	color	Scale bar and its label colour
scale_bar_thickness	number	2.0	pt	Scale bar line width
scale_bar_pad	number	0.05	fraction of the panel	Distance of the bar from the panel edges
scale_bar_label	true / false	True		Print the length above the bar
scale_bar_fontsize	number	6.0	pt	Scale bar label size
show_channel_labels	true / false	False		Print the channel names, in their tint, in the upper left
channel_label_fontsize	number	6.0	pt	Channel name size
channel_label_box	true / false	False		Put a dark box behind the channel names (keeps them readable on a busy image)
channel_label_box_color	colour	black	color	Colour of that box
channel_label_box_alpha	number	0.6	[0-1] opacity	Opacity of that box
labels_title	text	auto		Panel title
title_size	number	8.0	pt	Panel title size
frame	true / false	False		Draw a frame around the image
frame_color	colour	black	color	Frame colour
frame_width	number	0.5	pt	Frame line width

interval_track

fig_atlas_omics.renderers:render_interval_track

Key	Type	Default	Unit	What it does
start_col	text	start		Column with the interval start (bp, 1-based)
end_col	text	end		Column with the interval end (bp)
kind_col	text	kind		Column with the kind (sets colour and legend entry)
label_col	text	label		Column with the text beside an interval (none: no text)
kind_order	list	auto		Kinds in legend order (default: order in the data)
x_min	number	auto	bp	Left end of the window (both x_min and x_max; none: the data extent)
x_max	number	auto	bp	Right end of the window
max_rows	integer	3	rows	Most rows — raise if labels overlap on one row
row_gap_frac	number	0.01	fraction of the window	Smallest gap between two intervals (with their labels) on one row
kind_colors	mapping	{}	hex color	Colour per kind
kind_labels	mapping	{}		Legend text per kind
default_color	colour	#6b7280	hex color	Colour of kinds without one
bar_height	number	0.45	fraction of a row	Box height
bar_alpha	number	0.85	[0-1] opacity	Box opacity
bracket_kinds	list	[]		Kinds drawn as a bracket (a line with end ticks) instead of a box
bracket_width	number	0.8	pt	Bracket line width
open_kinds	list	[]		Kinds whose edges are open: no end ticks, a dotted line past both ends
open_extend_frac	number	0.04	fraction of the window	Length of that dotted line past each end — raise to stress that the edge is uncertain
open_style	text	:		Line style of that dotted line (matplotlib)
point_frac	number	0.002	fraction of the window	Intervals shorter than this are drawn as a triangle
point_edge_width	number	0.0	pt	Triangle outline width (0: filled only)
point_size	number	4.0	pt	Triangle marker size
label_size	number	5.5	pt	Label size
label_pad_frac	number	0.005	fraction of the window	Gap between an interval and its label (label right of it)
label_char_em	number	0.6	em per character	Estimated text width per character (packing only) — raise if labels on one row touch
text_color	colour	#111827	hex color	Label colour
show_legend	true / false	True		Show a legend of the kinds drawn
legend_loc	text	upper left		Legend location (matplotlib loc)
legend_anchor	list	[1.0, 1.0]	axes fraction [x, y]	Legend anchor point
legend_frameon	true / false	False		Draw a frame around the legend
legend_fontsize	number	style typography.legend_fontsize (else CODE_DEFAULT)	pt	Legend text font size — lower if the legend covers data
labels_ylabel	text	auto		Track name left of the track (none: no name)
axes_label_size	number	auto	pt	Track name size (default: rcParams)

jaccard_heatmap

fig_atlas.renderers:render_jaccard_heatmap

Key	Type	Default	Unit	What it does
row_col	text	pattern_class		Column giving the matrix rows
col_col	text	concordance_class		Column giving the matrix columns
value_col	text	jaccard		Column coloured in each cell
count_col	text	n_shared_terms		Column with the count printed in each cell
row_order	list	auto		Row order (default: order in the data)
col_order	list	auto		Column order (default: order in the data)
cmap	colormap	Reds		Colormap of the cells
vmin	number	0.0	value units	Lower end of the colour scale
vmax	number	auto	value units	Upper end of the colour scale (default: data maximum)
blank_when_count_zero	true / false	True		Leave cells with a zero count blank
blank_color	colour	white	color	Colour of blank cells
show_colorbar	true / false	True		Show the colourbar
colorbar_label	text	Jaccard		Colourbar title
colorbar_loc	one of right, left, top, bottom	right		Side of the colourbar
colorbar_shrink	number	0.8	fraction of the axes height	Colourbar length
cell_text_format	text	{value:.2f}({count:d})		Cell text; fields value and count
cell_text_color	text	black		Cell text colour, or 'auto' for white on dark cells
cell_text_size	number	computed	pt	Cell text size (default tick_label_size)
cell_border_color	colour	white	color	Grid line colour between cells
cell_border_width	number	1.0	pt	Grid line width between cells
labels_title	text	Jaccard Heatmap		Panel title
xtick_rotation	number	45	degrees	Column label rotation
title_size	number	13	pt	Panel title font size
axes_label_size	number	11	pt	Colourbar title font size
tick_label_size	number	8	pt	Row and column label font size

line_band

fig_atlas.renderers:render_line_band

Key	Type	Default	Unit	What it does
x_col	text	x		Column with the x values (numeric, or categories with x_order)
y_col	text	y		Column with the values (replicates), or the centre when aggregate is none
group_col	text	auto		Column splitting the lines (default: one line)
group_order	list	auto		Group order in drawing and legend (default: order in the data)
x_order	list	auto		Category order on x; set it to treat x as categories
aggregate	one of mean, median, none	mean		Centre of each (group, x): mean or median of the replicates, or none for summarised rows
error	one of sem, sd, ci95, none	sem		Band around the centre: standard error, standard deviation, 95% t-interval, or none
lower_col	text	auto		Lower band edge column (aggregate none)
upper_col	text	auto		Upper band edge column (aggregate none)
group_colors	mapping	{}	hex color	Colour per group (default: matplotlib cycle)
group_labels	mapping	{}		Legend label per group
line_width	number	1.2	pt	Centre line width
line_style	text	-		Centre line style (matplotlib)
marker	text	o		Marker at each x on the line ('' for none)
marker_size	number	3.0	pt	Line marker size
band_alpha	number	0.25	[0-1] opacity	Band opacity — lower when bands overlap
band_edge_width	number	0.0	pt	Outline width of the band (0: none)
show_points	true / false	False		Overlay the replicate values as points
point_size	number	8.0	pt^2 (marker area)	Replicate point size
point_alpha	number	0.6	[0-1] opacity	Replicate point opacity
point_jitter	number	0.0	x units (categories are 1 apart)	Horizontal scatter of the replicate points
point_seed	integer	0	random seed	Seed of the jitter (fixed for reproducible output)
x_log	true / false	False		Log-scaled x axis (numeric x)
x_min	number	auto	data coords	Lower x limit (both x_min and x_max needed)
x_max	number	auto	data coords	Upper x limit
y_min	number	auto	data coords	Lower y limit (both y_min and y_max needed)
y_max	number	auto	data coords	Upper y limit
zero_line	true / false	False		Draw y = 0
zero_line_color	colour	#9ca3af	hex color	y = 0 line colour
zero_line_width	number	0.5	pt	y = 0 line width
grid	true / false	False		Draw a background grid
grid_alpha	number	0.3	[0-1] opacity	Grid opacity
spine_width	number	auto	pt	Axis line width (default: rcParams)
hide_top_right	true / false	True		Hide the top and right axis lines
labels_title	text	auto		Panel title
labels_xlabel	text	computed		x-axis title (default: x_col)
labels_ylabel	text	computed		y-axis title (default: y_col)
title_size	number	style typography.title_size (else 8.0)	pt	Panel title font size — lower if the title wraps or crowds the panel
axes_label_size	number	auto	pt	Axis title size (default: rcParams)
tick_label_size	number	auto	pt	Tick label size (default: rcParams)
show_legend	true / false	True		Show the group legend (only with a group_col)
legend_loc	text	best		Legend location (matplotlib loc)
legend_fontsize	number	computed	pt	Legend font size (default: tick_label_size)
legend_frameon	true / false	False		Draw a frame around the legend

ma_plot

fig_atlas_omics.renderers:render_ma_plot

Key	Type	Default	Unit	What it does
padj_threshold	number	0.05	adjusted P	padj cut-off for up / down points
log2fc_threshold	number	0.585	log2 fold change	|log2FC| cut-off for up / down points (0.585 = 1.5-fold)
up_color	colour	#ff0000	hex color	Colour of up points
down_color	colour	#0000ff	hex color	Colour of down points
ns_color	colour	#808080	hex color	Colour of non-significant points
dot_size	number	10	pt^2 (marker area)	Point size
dot_alpha	number	0.5	[0-1] opacity	Point opacity
show_cutoff_lines	true / false	True		Draw y = 0 and +/- log2fc_threshold lines
cutoff_line_color	colour	black	color	Reference line colour
cutoff_line_style	text	--		Style of the threshold lines (matplotlib)
cutoff_line_width	number	1	pt	Reference line width
cutoff_line_alpha	number	0.5	[0-1] opacity	Reference line opacity
x_min	number	auto	log10 mean (data coords)	Lower x limit
x_max	number	auto	log10 mean (data coords)	Upper x limit
y_min	number	auto	log2 fold change	Lower y limit
y_max	number	auto	log2 fold change	Upper y limit
labels_title	text	MA Plot		Panel title
labels_xlabel	text	log10(Mean Accessibility)		x-axis title
labels_ylabel	text	Log2 Fold Change		y-axis title
title_size	number	13	pt	Panel title font size
axes_label_size	number	11	pt	Axis title font size
tick_label_size	number	8	pt	Tick and legend font size
show_legend	true / false	True		Show the legend
legend_position	text	best		Legend anchor (matplotlib loc)

motif_architecture_table

fig_atlas_omics.renderers:render_motif_architecture_table

Key	Type	Default	Unit	What it does
table_title	text	Key Transcriptional Driver Motifs: Sequence Logos, Statistics & Known Binding Partners		Title above the motif table
font_family	text	DejaVu Sans		Font of the table text
title_size	number	11.5	pt	Table title size
header_size	number	9.5	pt	Column header size
text_size	number	8.5	pt	Cell text size

motif_dotplot

fig_atlas_omics.renderers:render_motif_dotplot

Key	Type	Default	Unit	What it does
term_col	text	motif		Column with the motif (row) names
class_col	text	pattern_class		Column with the condition (column) names
value_col	text	log2fc		Column coloured: log2 fold enrichment
p_col	text	neg_log10_p		Column sized: -log10(P)
class_order	list	auto		Column order (default: order in the data)
term_order	list	auto		Row order (default: order in the data)
condition_rename_map	mapping	{}		Display label per condition
fc_cmap	colormap	RdBu_r		Diverging colormap of the fold enrichment
fc_min	number	-2.0	log2 fold enrichment	Lower colour limit
fc_max	number	2.0	log2 fold enrichment	Upper colour limit
na_color	colour	#cccccc	hex color	Colour of the placeholder dot in empty cells
show_colorbar	true / false	True		Show the colourbar
colorbar_label	text	log2 fold enrichment		Colourbar title
colorbar_loc	one of right, left, top, bottom	computed		Side of the colourbar (default: opposite the motif labels)
colorbar_shrink	number	0.6	fraction of the axes height	Colourbar length
size_min	number	6.0	pt^2 (marker area)	Dot area at -log10(P) = 0
size_scale	number	30.0	pt^2 per -log10(P) unit	Added dot area per -log10(P) unit — lower if neighbouring dots overlap
na_size	number	computed	pt^2 (marker area)	Placeholder dot size (default 0.4 x size_min)
dot_alpha	number	0.9	alpha [0-1]	Dot opacity
dot_edgecolor	colour	#555555	hex color	Dot outline colour
dot_edgewidth	number	0.5	pt	Dot outline width
show_size_legend	true / false	True		Show the dot size legend
size_legend_title	text	-log10(P)		Size legend title
size_legend_loc	text	best		Size legend location (matplotlib loc string)
size_legend_values	list	auto	-log10(P)	Values shown in the size legend (default 0, 5, 10)
show_grid	true / false	True		Draw horizontal grid lines
grid_color	colour	#eeeeee	hex color	Grid line colour
term_label_side	one of left, right	left		Side of the motif labels
label_margin_pad	number	1.2	multiple of the measured label width	Room left for the motif labels — raise if labels clip the canvas edge
label_margin_cap	number	0.5	fraction of the panel width	Largest label margin
min_plot_frac	number	0.3	fraction of the panel width	Smallest width kept for the dots
colorbar_margin	number	0.1	fraction of the panel width	Left margin for the colourbar when the labels are on the right
labels_title	text	Motif Enrichment		Panel title
labels_subtitle	text	auto		Second line under the title
title_pad	number	24.0	pt	Gap between title and axes
xtick_rotation	number	45	degrees	Condition label rotation
xtick_ha	one of left, center, right	right		Condition label horizontal alignment
xtick_rotation_mode	text	auto		matplotlib rotation_mode for the condition labels ('anchor' or 'default')
xtick_fontsize	number	computed	pt	Condition label size (default tick_label_size)
term_fontsize	number	computed	pt	Motif label size (default tick_label_size)
title_size	number	13	pt	Panel title font size
subtitle_size	number	9	pt	Subtitle font size
axes_label_size	number	11	pt	Colourbar title font size
tick_label_size	number	8	pt	Tick label font size

multi_group_heatmap

fig_atlas.renderers:render_multi_group_heatmap

Key	Type	Default	Unit	What it does
gene_label_col	text	gene_label		Column with the row (gene) labels
sample_columns	list	auto		Sample columns to show (default: every numeric column)
sample_groups	mapping	auto		Group name -> sample columns; orders and groups the columns
sample_rename_map	mapping	{}		Display label per raw sample name
cluster_rows	true / false	False		Cluster the rows and draw the row dendrogram
linkage	text	average		scipy linkage method (average, complete, ward, ...)
metric	text	euclidean		scipy distance metric for the clustering
dendro_width	number	0.12	fraction of the axes width	Width of the row dendrogram
cmap	colormap	RdBu_r		Colormap of the z-scores
z_auto	true / false	True		Symmetric colour limits from the data; set false to use z_min/z_max
z_min	number	-2.0	z-score	Lower colour limit when z_auto is false
z_max	number	2.0	z-score	Upper colour limit when z_auto is false
show_colorbar	true / false	True		Show the colourbar
colorbar_pad	number	computed	fraction of the axes width	Gap between heatmap and colourbar (default 0.15 with gene labels and dendrogram, else 0.02) — increase to widen the gap between heatmap and colorbar
group_colors	mapping	auto	hex color	Strip colour per sample group
show_group_bar	true / false	True		Show the group colour strip (columns stay grouped when off)
group_bar_height	number	0.03	fraction of the axes height	Strip height
group_bar_position	one of top, bottom	top		Strip above or below the heatmap
margin_left	number	auto	[0-1] fraction of the figure	Left edge of the heatmap block (default: matplotlib's figure.subplot.left)
margin_right	number	auto	[0-1] fraction of the figure	Right edge of the heatmap block, colour bar outside it (default: matplotlib's) — lower if the colour bar's title is cut off
margin_bottom	number	auto	[0-1] fraction of the figure	Bottom edge of the heatmap block (default: matplotlib's) — raise if the sample names below the heatmap are cut off
margin_top	number	auto	[0-1] fraction of the figure	Top edge of the heatmap block (default: matplotlib's)
show_group_legend	true / false	True		Show the group legend
show_gene_labels	true / false	True		Show the row labels
gene_fontsize	number	computed	pt	Row label size (default tick_label_size)
show_col_labels	true / false	True		Show the column labels
xtick_rotation	number	90	degrees	Column label rotation
labels_title	text	auto		Panel title
title	text	auto		Older name of labels_title, used when labels_title is not set
title_size	number	13	pt	Panel title font size
axes_label_size	number	11	pt	Colourbar title font size
tick_label_size	number	8	pt	Tick label font size

paired_dumbbell

fig_atlas.renderers:render_paired_dumbbell

Key	Type	Default	Unit	What it does
c_human	colour	#2563EB	hex color	Human marker colour
c_mouse	colour	#DC2626	hex color	Mouse marker colour
c_link	colour	#94A3B8	hex color	Line joining the two species of a condition
marker_size	number	90	pt^2 (marker area)	Marker size
marker_edgewidth	number	0.8	pt	Marker outline width
link_linewidth	number	2.0	pt	Width of the joining line
grid_linewidth	number	0.8	pt	Grid line width
linthresh	number	10.0	count (data coords)	symlog x: counts within +/- linthresh are drawn linearly
rna_xlim	list	[-1.5, 1200]	data coords [min, max]	x range of the RNA (DEG) column
rna_xticks	list	[0, 10, 100, 1000]	data coords	RNA tick positions
rna_xticklabels	list	['0', '$10^1$', '$10^2$', '$10^3$']		RNA tick labels
atac_xlim	list	[-1.5, 25000]	data coords [min, max]	x range of the ATAC (DA) column
atac_xticks	list	[0, 10, 100, 1000, 10000]	data coords	ATAC tick positions
atac_xticklabels	list	['0', '$10^1$', '$10^2$', '$10^3$', '$10^4$']		ATAC tick labels
xlabel	text	Significant Features (Count)		x-axis title
shared_xlabel	true / false	False		One x title under both columns instead of one per column
shared_xlabel_y	number	-0.14	figure fraction below the axes	Position of the shared x title
y_margin	number	auto	rows (data coords)	Empty room above and below the condition rows
annot_fontsize	number	8.0	pt	Count label size
annot_offset_pts	number	7	pt	Distance of the count labels from their marker
mouse_annot_below	true / false	False		Put mouse counts below their marker (human stays above)
header_fontsize	number	12.5	pt	Assay column header size
header_pad	number	8	pt	Gap between header and plot
ylabel_fontsize	number	11.0	pt	Row title (up/down-regulated) size
ylabel_pad	number	8	pt	Gap between row title and tick labels
ytick_fontsize	number	9.8	pt	Condition label size
xtick_fontsize	number	9.0	pt	x tick label size
xlabel_fontsize	number	9.5	pt	x title size
hide_inner_yticklabels	true / false	False		Show condition labels only on the left column
show_right_row_label	true / false	True		Repeat the row title, rotated, right of the right column
facet_layout	one of 2x2, 4x1	2x2		Facet arrangement: 2x2 = directions in rows, assays in columns; 4x1 = all four stacked in one column (assay by assay), for a single journal column — 4x1 when the figure spans one column and the 2x2 facets crowd
legend_fontsize	number	9.5	pt	Legend text size
legend_markersize	number	9	pt	Legend marker size
legend_edgecolor	colour	#cbd5e1	hex color	Legend frame colour
legend_row_ratio	number	0.08	x a plot row's height	Height of the legend row under the plots
hspace	number	0.35	fraction of a row's height	Gap between the up and down rows
wspace	number	0.28	fraction of a column's width	Gap between the RNA and ATAC columns
left_inset	number	0.0	[0-1] fraction of the slot width	Empty strip on the left of the slot — raise if the row titles clip at the left
extend_right	number	0.0	fraction of the plot width	Stretch the plots rightwards by this share (to end where a neighbouring panel ends)

pathway_evidence_dotplot

fig_atlas_omics.renderers:render_pathway_evidence_dotplot

Key	Type	Default	Unit	What it does
evidence_colors	mapping	{}	hex color	Colour per evidence type, merged over the defaults (ORA, GSEA, ORA + GSEA)
evidence_labels	mapping	{}		Legend text per evidence type
size_per_gene	number	0.6	pt^2 per member gene	Dot area added per member gene — lower if large terms' dots overlap
size_offset	number	4	pt^2 (marker area)	Dot area of a term with no genes
dot_alpha	number	0.9	alpha [0-1]	Dot opacity
dot_edgecolor	colour	#333333	hex color	Dot outline colour
dot_edgewidth	number	0.4	pt	Dot outline width
min_rows	integer	0	rows	Reserve at least this many rows (keeps panels the same height)
empty_note	text	auto		Text in the empty rows when there are fewer terms than min_rows; '{n}' = count
empty_note_color	colour	#6b7280	hex color	Empty-row note colour
empty_note_wrap_width	integer	40	characters	Wrap the empty-row note at this width
ylabel_wrap_width	integer	42	characters	Wrap term names at this width
term_fontsize	number	6	pt	Term name size
xlabel	text	-log10(adjusted P)		x-axis title
xlim_headroom	number	0.12	fraction of the largest x	Space added past the largest dot — raise if the right-most dot is clipped
grid_linewidth	number	0.4	pt	Grid line width
legend_loc	text	upper left		Legend location (matplotlib loc string)
legend_bbox	list	[1.02, 1.0]	axes fraction (x, y)	Legend anchor; default sits right of the axes
legend_fontsize	number	5.5	pt	Legend font size
legend_labelspacing	number	0.6	font-size units	Vertical space between legend entries
legend_marker_size	number	4	pt	Marker size of the evidence entries
size_legend_values	list	[20, 100]	genes	Gene counts shown in the size legend
size_legend_title	text	genes		Word after each size legend value
labels_title	text	auto		Panel title
title_pad	number	5	pt	Gap between title and axes
title_size	number	8	pt	Panel title font size
axes_label_size	number	7	pt	Axis title font size
tick_label_size	number	6	pt	Tick label font size

pathway_test_matrix

fig_atlas_omics.renderers:render_pathway_test_matrix

Key	Type	Default	Unit	What it does
term_order	list	auto		Row order top to bottom (default: order of first appearance)
test_order	list	auto		Column order (default: order of first appearance)
test_labels	mapping	{}		Column label per test key
min_rows	integer	0	rows	Keep the row spacing of this many rows for short lists (empty slots at the bottom)
term_fontsize	number	6	pt	Term label size
ylabel_wrap_width	integer	42	characters	Wrap term labels at this width
xtick_fontsize	number	6	pt	Column label size
xtick_rotation	number	30	degrees	Column label rotation
column_header	text	auto		Text over the test columns
column_header_pad	number	0.02	axes fraction	Gap between the matrix and the column header
column_header_fontsize	number	5.5	pt	Column header size
column_header_color	colour	#334155	hex color	Column header colour
cmap	colormap	viridis		Colormap for -log10 adjusted P
vmin	number	computed	-log10 adjusted P	Colour floor (default -log10(0.05))
vmax	number	computed	-log10 adjusted P	Colour ceiling (default: from the data)
size_per_share	number	600.0	pt^2 per unit share	Dot area per share of class genes — lower if dots overlap
size_min	number	4.0	pt^2 (marker area)	Smallest dot
hollow_color	colour	#ffffff	hex color	Fill of tested but not significant dots
hollow_label	text	n.s.		Legend text for hollow dots
dot_edgecolor	colour	#333333	hex color	Dot outline colour
dot_edgewidth	number	0.4	pt	Dot outline width
dot_alpha	number	0.9	[0-1] opacity	Dot opacity
grid_linewidth	number	0.4	pt	Grid line width
labels_title	text	auto		Panel title (none = no title)
title_size	number	8	pt	Panel title font size
title_pad	number	5	pt	Gap between title and matrix
cbar_label	text	-log10(adjusted P)		Colourbar title
cbar_label_size	number	6	pt	Colourbar title size
cbar_tick_size	number	5.5	pt	Colourbar tick size
cbar_outline_width	number	0.5	pt	Colourbar outline width
size_legend_values	list	[0.05, 0.15]	share of class genes	Shares shown in the size legend
size_legend_title	text	Share of class genes		Size legend title
legend_fontsize	number	5.5	pt	Legend text size
legend_loc	text	lower left		Legend anchor point (matplotlib loc)
legend_bbox	list	[1.04, 0.0]	axes fraction (x, y)	Where legend_loc is placed
legend_labelspacing	number	0.8	x font size	Vertical spacing of legend entries
legend_ncol	integer	1	columns	Legend columns
legend_columnspacing	number	1.0	x font size	Horizontal spacing of legend columns
empty_note	text	auto		Note shown in the empty slots when min_rows exceeds the term count
empty_note_x	number	-0.6	data coords	x position of the empty-slot note
empty_note_wrap_width	integer	30	characters	Wrap the note at this width
empty_note_color	colour	#6b7280	hex color	Note colour

pca

fig_atlas.renderers:render_pca

Key	Type	Default	Unit	What it does
n_genes	integer	500	genes	Most variable genes used for the PCA
transform	one of log2, log1p, none	log2		Transform of the counts before the PCA
scaling	one of standard, none	standard		'standard': centre and scale each gene; otherwise centre only
x_pc	integer	1	component number	Component on the x axis
y_pc	integer	2	component number	Component on the y axis
sample_columns	list	auto		Columns to use as samples (default: every numeric column that is not a statistic such as padj or log2FC)
sample_groups	mapping	auto		Group name -> its sample columns; points are coloured by group, with a legend
group_colors	mapping	{}	hex color	Colour per group (default: matplotlib tab10 by group)
legend_loc	text	best		Group legend location (matplotlib loc)
sample_rename_map	mapping	{}		Display label per raw sample name
point_size	number	80	pt^2 (marker area)	Sample point size
show_labels	true / false	True		Label each sample point
title	text	PCA — Sample Expression		Panel title
title_size	number	10	pt	Panel title font size
axes_label_size	number	8	pt	Axis title font size
tick_label_size	number	7	pt	Tick and point label font size

peak_feature_composition

fig_atlas_omics.renderers:render_peak_feature_composition

Key	Type	Default	Unit	What it does
geneset_col	text	GeneSet		Column with the gene set (one facet or bar group each)
geneset_order	list	auto		Gene set order (default: order in the data)
geneset_rename_map	mapping	{}		Display title per gene set
feature_col	text	Feature		Column with the peak feature category
feature_order	list	auto		Feature order (default: order in the data); first is bottom in the composition bars
odds_ratio_col	text	OddsRatio		Enrichment: odds ratio column
fdr_col	text	p_adjust		Enrichment: adjusted P column
da_pct_col	text	DA_Pct		Composition: percentage of DA peaks per feature
background_pct_col	text	Background_Pct		Composition: percentage of background peaks per feature
fdr_max	number	0.05	FDR	Bars at or below this FDR use sig_color
sig_color	colour	#e57373	hex color	Colour of significant bars
ns_color	colour	#9e9e9e	hex color	Colour of non-significant bars
bar_height	number	0.68	fraction of the row	Bar thickness
bar_edgecolor	colour	black	color	Enrichment bar outline colour
bar_edgewidth	number	0.5	pt	Enrichment bar outline width
shared_xlim	true / false	True		One zero-centred x range for every facet, so bar lengths compare across facets
xlim_pad	number	1.15	multiple of the largest |log2 OR|	Margin of the shared x range
xlim	list	auto	data coords [min, max]	Explicit x range; overrides shared_xlim (use it to align separate calls)
wspace	number	0.08	fraction of the mean facet width	Gap between facets
xlabel_text	text	log2(Odds Ratio) vs background		x-axis title of the enrichment facets
feature_colors	mapping	auto	hex color	Colour per feature (default: built-in palette)
bar_width	number	0.7	x units (one bar = 1)	Composition bar width
group_gap	number	1.0	x units	Extra gap between gene set groups
edge_color	colour	white	color	Outline between stacked segments
edge_width	number	0.5	pt	Segment outline width
ylabel_text	text	% of peaks		y-axis title of the composition chart
show_legend	true / false	True		Show the legend
legend_loc	text	computed		Legend location (default 'best' for enrichment, 'center left' for composition)
labels_title	text	computed		Figure title (each chart has its own default)
title_size	number	13	pt	Title font size
axes_label_size	number	11	pt	Axis title font size
tick_label_size	number	8	pt	Tick label font size

peak_feature_enrichment

fig_atlas_omics.renderers:render_peak_feature_enrichment

Key	Type	Default	Unit	What it does
geneset_col	text	GeneSet		Column with the gene set (one facet or bar group each)
geneset_order	list	auto		Gene set order (default: order in the data)
geneset_rename_map	mapping	{}		Display title per gene set
feature_col	text	Feature		Column with the peak feature category
feature_order	list	auto		Feature order (default: order in the data); first is bottom in the composition bars
odds_ratio_col	text	OddsRatio		Enrichment: odds ratio column
fdr_col	text	p_adjust		Enrichment: adjusted P column
da_pct_col	text	DA_Pct		Composition: percentage of DA peaks per feature
background_pct_col	text	Background_Pct		Composition: percentage of background peaks per feature
fdr_max	number	0.05	FDR	Bars at or below this FDR use sig_color
sig_color	colour	#e57373	hex color	Colour of significant bars
ns_color	colour	#9e9e9e	hex color	Colour of non-significant bars
bar_height	number	0.68	fraction of the row	Bar thickness
bar_edgecolor	colour	black	color	Enrichment bar outline colour
bar_edgewidth	number	0.5	pt	Enrichment bar outline width
shared_xlim	true / false	True		One zero-centred x range for every facet, so bar lengths compare across facets
xlim_pad	number	1.15	multiple of the largest |log2 OR|	Margin of the shared x range
xlim	list	auto	data coords [min, max]	Explicit x range; overrides shared_xlim (use it to align separate calls)
wspace	number	0.08	fraction of the mean facet width	Gap between facets
xlabel_text	text	log2(Odds Ratio) vs background		x-axis title of the enrichment facets
feature_colors	mapping	auto	hex color	Colour per feature (default: built-in palette)
bar_width	number	0.7	x units (one bar = 1)	Composition bar width
group_gap	number	1.0	x units	Extra gap between gene set groups
edge_color	colour	white	color	Outline between stacked segments
edge_width	number	0.5	pt	Segment outline width
ylabel_text	text	% of peaks		y-axis title of the composition chart
show_legend	true / false	True		Show the legend
legend_loc	text	computed		Legend location (default 'best' for enrichment, 'center left' for composition)
labels_title	text	computed		Figure title (each chart has its own default)
title_size	number	13	pt	Title font size
axes_label_size	number	11	pt	Axis title font size
tick_label_size	number	8	pt	Tick label font size

sample_metric_bars

fig_atlas.renderers:render_sample_metric_bars

Key	Type	Default	Unit	What it does
group_order	list	auto		Group order, left to right (default: order in the data)
group_colors	mapping	{}		Bar colour per group (unlisted groups are grey)
group_labels	mapping	{}		Display label per group
bar_width	number	0.8	x units (one sample = 1)	Bar width
group_gap	number	0.6	x units	Extra gap between groups — raise to separate the groups more
edgecolor	colour	none	color	Bar outline colour
ylim	list	auto	data coords [min, max]	y-axis range (default: data)
spine_width	number	0.6	pt	Axis spine width
ref_lines	list	[]		Horizontal reference lines: list of {y, label, color, style, width}
ref_label_x	number	1.0	axes fraction	x position of the reference line labels
ref_label_fontsize	number	5.0	pt	Reference line label size
show_values	true / false	auto		Print each bar's value above it
value_fmt	text	{:.2f}		Format string of the printed values
value_fontsize	number	4.8	pt	Printed value size
title	text	auto		Panel title
ylabel	text	auto		y-axis title
group_label_rotation	number	0	degrees	Group label rotation
title_pad	number	3.0	pt	Gap between title and axes
title_size	number	6.5	pt	Panel title font size
axes_label_size	number	6.0	pt	Axis title font size
tick_label_size	number	5.5	pt	y tick label font size
group_label_fontsize	number	5.5	pt	Group label font size

segment_array

fig_atlas_omics.renderers:render_segment_array

Key	Type	Default	Unit	What it does
length_col	text	length_bp		Column with each segment's length (bp)
kind_col	text	kind		Column with each segment's kind (sets its colour)
label_col	text	label		Column with the text above a segment (none: no labels)
sublabel_col	text	auto		Column with the text below a segment, e.g. source coordinates
strand_col	text	strand		Column with + / - (an arrow pointing right / left); other values: a box
group_col	text	auto		Column grouping consecutive segments under one bracket and label
inner_label_col	text	auto		Column with the name written inside a segment (under it if it does not fit)
span_col	text	auto		Column grouping consecutive segments under one direction arrow
span_label_col	text	auto		Column with the text over a span arrow, e.g. source coordinates
span_strand_col	text	auto		Column with + / - for the span arrow direction (default: strand_col)
scale	one of linear, sqrt, log	linear		How length maps to width — sqrt or log when one segment is far longer than the rest (e.g. a BAC next to a linker)
min_frac	number	0.012	fraction of the row width	Smallest width a segment is drawn at — raise if short pieces disappear
flank_kinds	list	['host']		Kinds drawn as host flanks at a fixed width (length ignored)
flank_frac	number	0.12	fraction of the row width	Width of each host flank
gap_kinds	list	['copy_gap']		Kinds drawn as a thin line instead of a box (unmapped linkers)
x_pad_frac	number	0.01	fraction of the row width	Blank margin left and right of the row
kind_colors	mapping	{}	hex color	Fill colour per kind
default_color	colour	#9ca3af	hex color	Fill of kinds without a colour
edge_color	colour	#1f2937	hex color	Segment outline colour
edge_width	number	0.4	pt	Segment outline width (0: none)
bar_height	number	0.28	axes data units (row is 0-1 high)	Height of a segment box — raise for a bolder row
bar_y	number	0.45	axes data units (0-1)	Height of the row centre
arrow_head_frac	number	0.3	fraction of the segment width	Length of an arrow head on stranded segments
arrow_head_max_frac	number	0.025	fraction of the row width	Longest an arrow head may be — lower for blunter arrows on long segments
gap_color	colour	#6b7280	hex color	Colour of gap lines
gap_width	number	0.8	pt	Width of gap lines
gap_style	text	:		Line style of gap lines (matplotlib)
separator_width	number	0.6	pt	Width of the tick drawn between adjacent segments (0: none)
separator_color	colour	#111827	hex color	Colour of the ticks between segments
inner_label_size	number	6.0	pt	Size of the names inside segments
inner_label_weight	text	normal		Font weight of the names inside segments
inner_text_dark	colour	#111827	hex color	Name colour on light fills
inner_text_light	colour	#ffffff	hex color	Name colour on dark fills
inner_luminance_cut	number	0.5	relative luminance [0-1]	Fills darker than this get the light name colour
inner_label_margin	number	0.9	fraction of the segment width	Share of a segment's width a name may use before it moves under the segment
inner_fallback	one of above, below	below		Where a name too wide for its segment goes: above the bar, or under it (after any label there)
label_char_em	number	0.6	em per character	Estimated text width per character (fit test only) — raise if names spill over their segment
span_pad	number	0.07	axes data units	Gap between the bar and the span arrows
span_inset_frac	number	0.003	fraction of the row width	Gap left at each end of a span arrow so neighbouring arrows do not touch
span_color	colour	#111827	hex color	Span arrow colour
span_line_width	number	0.6	pt	Span arrow line width
span_head	number	5.0	pt	Span arrow head size
span_label_size	number	5.0	pt	Size of the text over span arrows
span_label_pad	number	0.02	axes data units	Gap between a span arrow and its text
label_size	number	6.0	pt	Size of the labels above segments
label_pad	number	0.04	axes data units	Gap between a bar and its label
label_min_frac	number	0.0	fraction of the row width	Segments narrower than this get no label above — raise to thin out crowded labels
sublabel_size	number	5.0	pt	Size of the labels below segments
sublabel_rotation	number	0.0	degrees	Rotation of the labels below segments
sublabel_stagger	number	0.0	axes data units	Drop every second label below the bar by this much (0: one line) — raise when labels of neighbouring narrow segments touch
sublabel_min_frac	number	0.0	fraction of the row width	Segments narrower than this get no label below
flank_label_size	number	6.0	pt	Size of the host flank labels
flank_label_style	text	italic		Font style of the host flank labels
flank_label_pad	number	0.04	axes data units	Gap between a host flank and its label
group_bracket	true / false	True		Draw a bracket over each group
group_bracket_pad	number	0.06	axes data units	Gap between the bars and a group bracket
group_bracket_height	number	0.05	axes data units	Height of the bracket ends
group_bracket_width	number	0.5	pt	Bracket line width
group_bracket_color	colour	#374151	hex color	Bracket colour
group_label_size	number	6.0	pt	Size of the group labels
group_label_weight	text	bold		Font weight of the group labels
text_color	colour	#111827	hex color	Colour of all labels
labels_title	text	auto		Row title, at the top left (none: no title)
title_size	number	style typography.title_size (else 8.0)	pt	Panel title font size — lower if the title wraps or crowds the panel
title_loc	text	left		Title alignment (matplotlib loc)
title_pad	number	2.0	pt	Gap between the title and the row

signed_heatmap

fig_atlas.renderers:render_signed_heatmap

Key	Type	Default	Unit	What it does
cmap	colormap	RdBu_r		Diverging colormap for the signed values — any registered diverging map
vmax	number	10.0	value units (e.g. signed -log10 FDR)	Colour scale runs -vmax..+vmax; beyond is drawn saturated — lower to stretch contrast for weak values
nan_color	colour	#e5e7eb	hex color	Colour of missing (not tested) cells
origin	one of upper, lower	upper		'upper': first row on top; 'lower': first row at the bottom (to align with a 0..n-1 scatter)
ylim	list	auto	data coords [lo, hi]	Row range, to line up with another axes' rows
cell_edgecolor	colour	white	hex color	Cell border colour
cell_edgewidth	number	0.5	pt	Cell border width — 0 for no borders
frame_width	number	0.6	pt	Outer frame (spine) width
show_values	true / false	False		Print each cell's value
value_fmt	text	{:+.1f}		Python format for the printed values
value_fontsize	number	5.0	pt	Cell value font size — lower if values overflow cells
value_text_color_mode	one of threshold, contrast	threshold		'threshold': white text above value_dark_threshold; 'contrast': white or dark by contrast with the cell colour
value_dark_threshold	number	0.6	fraction of vmax	|value|/vmax above which text turns light (threshold mode) — lower if text on mid-dark cells is hard to read
value_light_color	colour	white	hex color	Text colour on dark cells
value_dark_color	colour	#111827	hex color	Text colour on light cells
muted_value_color	colour	#9ca3af	hex color	Text colour of muted values (e.g. not significant)
muted_value_style	one of normal, italic, oblique	italic		Font style of muted values
show_row_labels	true / false	True		Show row (feature) labels
row_label_side	one of left, right	left		Side the row labels sit on
row_label_style	one of normal, italic, oblique	normal		Row label font style (italic for gene names)
row_label_fontsize	number	6.0	pt	Row label font size — lower if labels overlap
row_separators	list	[]	row indices	Draw a horizontal line above each of these rows
row_separator_color	colour	#1f2937	hex color	Row separator colour
row_separator_width	number	0.8	pt	Row separator width
col_labels	list	auto		Column labels (default: the column names)
col_label_fontsize	number	5.5	pt	Column label font size
col_label_rotation	number	0	degrees	Column label rotation — 45 if labels collide
col_label_side	one of bottom, top	bottom		Side the column labels sit on
col_groups	list	auto		Column group headers: [[label, n_columns], ...] left to right
group_label_fontsize	number	6.0	pt	Column group header font size
group_label_weight	text	bold		Column group header font weight
group_label_pad	number	0.4	rows (data units)	Gap between the matrix and the group headers — raise if headers touch the column labels
group_separator_color	colour	#1f2937	hex color	Vertical line between column groups
group_separator_width	number	0.8	pt	Column group separator width

single_tf_expression_scatter_bar

fig_atlas_omics.renderers:render_single_tf_expression_scatter_bar

Key	Type	Default	Unit	What it does
n_cols	integer	computed	genes per row	Columns of the gene grid (default: up to 7)
hspace	number	0.4	fraction of a panel's height	Gap between grid rows
wspace	number	0.28	fraction of a panel's width	Gap between grid columns
gene_family_map	mapping	{}		Family tag shown under each gene's name (gene -> text)
family_wrap_width	integer	auto	characters	Wrap the family tag at this width
condition_colors	list	computed	hex colors in condition order	Colour per condition (default: grey, red, orange, purple, blue)
short_condition_labels	list	['Cont', 'D1', 'D3', '24h', '48h']		x labels of the conditions
bar_width	number	0.65	data units (conditions are 1 apart)	Bar width
bar_alpha	number	0.7	[0-1] opacity	Bar opacity
bar_edgewidth	number	0.8	pt	Bar outline width
errorbar_linewidth	number	0.8	pt	Error bar and cap line width
capsize	number	2.5	pt	Error bar cap length
show_points	true / false	True		Overlay each replicate as a point
point_size	number	24.0	pt^2 (marker area)	Replicate point size
point_edgewidth	number	0.6	pt	Replicate point outline width
point_jitter	number	0.12	data units	Horizontal scatter of the points
point_seed	integer	42	random seed	Seed for the jitter, so the layout is reproducible
show_anova	true / false	True		Print the one-way ANOVA P above each gene
anova_font_size	number	7.5	pt	ANOVA text size
show_asterisks	true / false	True		Mark conditions that differ from control with stars
star_font_size	number	9.5	pt	Star size
stat_test	one of welch, student, mannwhitney	welch		Test of each condition against control (Welch t-test, Student t-test, Mann-Whitney U)
stat_correction	one of none, bonferroni, holm, bh	none		Multiple-testing correction applied before the stars (bh = Benjamini-Hochberg FDR)
stat_correction_scope	one of gene, figure	gene		Correction family: each gene's comparisons, or every comparison in this grid
star_thresholds	list	[[0.001, '***'], [0.01, '**'], [0.05, '*']]	P (adjusted)	[threshold, symbol] pairs, ascending; a star needs P below the threshold
record_statistics	true / false	True		Save the test table with the figure (published as figure_NN_statistics/)
stats_table_name	text	tf_expression_tests		File name (no extension) of the saved test table
y_headroom	number	1.35	x the tallest bar	y range above the bars — raise if stars or the ANOVA text clip at the top
gene_title_size	number	10.5	pt	Gene name (panel title) size
title_pad	number	4	pt	Gap between gene name and plot
show_ylabel	true / false	True		Show the y-axis title
ylabel	text	Norm. Counts		y-axis title
ylabel_size	number	9.0	pt	y-axis title size
tick_label_size	number	8.0	pt	Tick label size
xtick_rotation	number	0	degrees	Condition label rotation
spine_width	number	0.8	pt	Axis line width

species_response_scatter

fig_atlas_omics.renderers:render_species_response_scatter

Key	Type	Default	Unit	What it does
category_order	list	auto		Drawing order of the categories (later on top)
colors	mapping	{}	hex color per category	Point colour per category
sizes	mapping	{}	pt^2 per category	Point size per category
alphas	mapping	{}	[0-1] per category	Point opacity per category
default_size	number	1.0	pt^2 (marker area)	Size of categories without one
default_alpha	number	0.5	[0-1] opacity	Opacity of categories without one
edgecolor	colour	none	color	Point outline
rasterized	true / false	True		Rasterize the points (smaller PDF for tens of thousands of points)
lim	number	6.0	log2 fold change (data coords)	Both axes run -lim..+lim — raise if many points pile on the edge
ticks	list	auto	data coords	Tick positions on both axes
zero_line_color	colour	#9ca3af	hex color	Colour of the x = 0 and y = 0 lines
zero_line_width	number	0.4	pt	Width of the zero lines
diagonal	true / false	True		Draw the y = x line
diagonal_color	colour	#6b7280	hex color	Colour of the y = x line
diagonal_width	number	0.4	pt	Width of the y = x line
diagonal_style	text	--		Line style of the y = x line (matplotlib)
spine_width	number	0.6	pt	Axis line and tick width
xlabel	text	auto		x-axis title
ylabel	text	auto		y-axis title
axes_label_size	number	6.5	pt	Axis title font size
tick_label_size	number	5.5	pt	Tick label font size
title	text	auto		Panel title
title_size	number	7.0	pt	Panel title font size
title_weight	text	bold		Panel title font weight
title_pad	number	2.0	pt	Gap between title and plot
annotations	list	[]		Lines of text at the top left (e.g. rho, n)
annotation_fontsize	number	5.5	pt	Annotation text size
annotation_xy	list	[0.03, 0.97]	axes fraction (x, y)	Position of the first annotation line
annotation_line_step	number	0.075	axes fraction	Spacing between annotation lines
annotation_color	colour	#111827	hex color	Annotation text colour

stacked_bar

fig_atlas.renderers:render_stacked_bar

Key	Type	Default	Unit	What it does
y_log	true / false	False		Log-scaled y axis
y_min	number	auto	data coords	Lower y limit (both y_min and y_max needed)
y_max	number	auto	data coords	Upper y limit
grid	true / false	False		Draw horizontal grid lines
grid_alpha	number	0.3	[0-1] opacity	Grid opacity
spine_width	number	auto	pt	Axis line width (default: rcParams)
hide_top_right	true / false	True		Hide the top and right axis lines
labels_title	text	auto		Panel title (none: no title)
labels_xlabel	text	computed		x-axis title (default: the x column's name)
labels_ylabel	text	computed		y-axis title (default: the y column's name)
title_size	number	8.0	pt	Panel title size
axes_label_size	number	auto	pt	Axis title size (default: rcParams)
tick_label_size	number	auto	pt	Tick label size (default: rcParams)
show_legend	true / false	True		Show the group legend (only with a group_col)
legend_loc	text	best		Legend location (matplotlib loc)
legend_fontsize	number	auto	pt	Legend font size (none: tick_label_size)
legend_frameon	true / false	False		Draw a frame around the legend
x_col	text	category		Column with the categories (one bar each)
stack_col	text	part		Column with the parts stacked in each bar
value_col	text	count		Column with the counts
x_order	list	auto		Bar order (default: order in the data)
stack_order	list	auto		Part order from the bottom up (default: order in the data)
x_labels	mapping	{}		Shown name per category (default: the category)
percent	true / false	True		Each bar as shares of 100 % (False: counts)
stack_colors	mapping	{}	hex color	Colour per part (default: matplotlib colour cycle)
stack_labels	mapping	{}		Legend label per part (default: the part)
bar_width	number	0.7	x units (bars are 1 apart)	Bar width
edge_color	colour	#ffffff	hex color	Line between the parts
edge_width	number	0.5	pt	Width of that line
x_tick_rotation	number	0.0	degrees	Rotation of the category names — raise (e.g. 45) when long names collide
legend_outside	true / false	True		Put the legend right of the bars (so it never covers them)
legend_anchor	list	[1.02, 0.5]	axes fraction [x, y]	Where the legend's left middle sits when outside — raise x for more gap from the bars

stacked_share_hbar

fig_atlas.renderers:render_stacked_share_hbar

Key	Type	Default	Unit	What it does
group_order	list	auto		Bar order top to bottom (default: the rows of counts)
category_order	list	auto		Segment order left to right (default: the columns of counts)
group_labels	mapping	{}		Display label per group (bar)
colors	mapping	{}	hex color per category	Segment colour per category
bar_height	number	0.7	data units (rows are 1 apart)	Bar thickness
edgecolor	colour	white	color	Line between segments
edgewidth	number	0.4	pt	Width of the line between segments
spine_width	number	0.6	pt	Axis line width
show_pct	true / false	True		Print each segment's share inside it
pct_min	number	8.0	% share	Smallest share that gets a label — raise if labels crowd narrow segments
pct_fmt	text	{:.0f}%		Python format of the share label
pct_fontsize	number	5.0	pt	Share label size
dark_categories	list	[]		Categories (dark fills) whose labels use pct_color_dark
pct_color_dark	colour	white	color	Label colour on dark segments
pct_color_light	colour	#111827	hex color	Label colour on light segments
show_total	true / false	True		Print each bar's total at its right end
total_fmt	text	n = {:,}		Python format of the total
total_fontsize	number	5.5	pt	Total label size
total_pad	number	0.01	fraction of the 100% width	Gap between bar end and total
xlabel	text	Share (%)		x-axis title
axes_label_size	number	6.5	pt	Axis title font size
tick_label_size	number	5.5	pt	Tick and group label font size
legend	true / false	True		Show the category legend
legend_labels	mapping	{}		Legend text per category
legend_ncol	integer	2	columns	Legend columns
legend_fontsize	number	5.5	pt	Legend text size
legend_loc	text	upper center		Legend anchor point (matplotlib loc)
legend_anchor	list	[0.5, -0.3]	axes fraction (x, y)	Where legend_loc is placed — lower y if the legend overlaps the x-axis title

survival

fig_atlas.renderers:render_survival

Key	Type	Default	Unit	What it does
group_col	text	auto		Column splitting the data into coloured groups (default: one group)
group_order	list	auto		Group order in drawing and legend (default: order in the data)
group_colors	mapping	{}	hex color	Colour per group (default: matplotlib colour cycle)
group_labels	mapping	{}		Legend label per group (default: the group value)
color	colour	#4b5563	hex color	Colour when there is no group_col
x_log	true / false	False		Log-scaled x axis
x_min	number	auto	data coords	Lower x limit (both x_min and x_max needed)
x_max	number	auto	data coords	Upper x limit
y_log	true / false	False		Log-scaled y axis
y_min	number	auto	data coords	Lower y limit (both y_min and y_max needed)
y_max	number	auto	data coords	Upper y limit
grid	true / false	False		Draw horizontal grid lines
grid_alpha	number	0.3	[0-1] opacity	Grid opacity
spine_width	number	auto	pt	Axis line width (default: rcParams)
hide_top_right	true / false	True		Hide the top and right axis lines
labels_title	text	auto		Panel title (none: no title)
labels_xlabel	text	computed		x-axis title (default: the x column's name)
labels_ylabel	text	computed		y-axis title (default: the y column's name)
title_size	number	8.0	pt	Panel title size
axes_label_size	number	auto	pt	Axis title size (default: rcParams)
tick_label_size	number	auto	pt	Tick label size (default: rcParams)
show_legend	true / false	True		Show the group legend (only with a group_col)
legend_loc	text	best		Legend location (matplotlib loc)
legend_fontsize	number	auto	pt	Legend font size (none: tick_label_size)
legend_frameon	true / false	False		Draw a frame around the legend
time_col	text	time		Column with the time to the event or to the last follow-up
event_col	text	event		Column: 1 (or True) if the event happened, 0 (or False) if censored
percent	true / false	True		Show survival in % (0-100) instead of a fraction (0-1)
line_width	number	1.2	pt	Curve width
show_censored	true / false	True		Mark censored subjects with a tick on the curve
censor_marker	text	\|		Censor mark (matplotlib marker)
censor_size	number	5.0	pt	Censor mark size

tf_expression_scatter_grid

fig_atlas_omics.renderers:render_tf_expression_scatter_grid

Key	Type	Default	Unit	What it does
n_cols	integer	computed	genes per row	Columns of the gene grid (default: up to 7)
hspace	number	0.4	fraction of a panel's height	Gap between grid rows
wspace	number	0.28	fraction of a panel's width	Gap between grid columns
gene_family_map	mapping	{}		Family tag shown under each gene's name (gene -> text)
family_wrap_width	integer	auto	characters	Wrap the family tag at this width
condition_colors	list	computed	hex colors in condition order	Colour per condition (default: grey, red, orange, purple, blue)
short_condition_labels	list	['Cont', 'D1', 'D3', '24h', '48h']		x labels of the conditions
bar_width	number	0.65	data units (conditions are 1 apart)	Bar width
bar_alpha	number	0.7	[0-1] opacity	Bar opacity
bar_edgewidth	number	0.8	pt	Bar outline width
errorbar_linewidth	number	0.8	pt	Error bar and cap line width
capsize	number	2.5	pt	Error bar cap length
show_points	true / false	True		Overlay each replicate as a point
point_size	number	24.0	pt^2 (marker area)	Replicate point size
point_edgewidth	number	0.6	pt	Replicate point outline width
point_jitter	number	0.12	data units	Horizontal scatter of the points
point_seed	integer	42	random seed	Seed for the jitter, so the layout is reproducible
show_anova	true / false	True		Print the one-way ANOVA P above each gene
anova_font_size	number	7.5	pt	ANOVA text size
show_asterisks	true / false	True		Mark conditions that differ from control with stars
star_font_size	number	9.5	pt	Star size
stat_test	one of welch, student, mannwhitney	welch		Test of each condition against control (Welch t-test, Student t-test, Mann-Whitney U)
stat_correction	one of none, bonferroni, holm, bh	none		Multiple-testing correction applied before the stars (bh = Benjamini-Hochberg FDR)
stat_correction_scope	one of gene, figure	gene		Correction family: each gene's comparisons, or every comparison in this grid
star_thresholds	list	[[0.001, '***'], [0.01, '**'], [0.05, '*']]	P (adjusted)	[threshold, symbol] pairs, ascending; a star needs P below the threshold
record_statistics	true / false	True		Save the test table with the figure (published as figure_NN_statistics/)
stats_table_name	text	tf_expression_tests		File name (no extension) of the saved test table
y_headroom	number	1.35	x the tallest bar	y range above the bars — raise if stars or the ANOVA text clip at the top
gene_title_size	number	10.5	pt	Gene name (panel title) size
title_pad	number	4	pt	Gap between gene name and plot
show_ylabel	true / false	True		Show the y-axis title
ylabel	text	Norm. Counts		y-axis title
ylabel_size	number	9.0	pt	y-axis title size
tick_label_size	number	8.0	pt	Tick label size
xtick_rotation	number	0	degrees	Condition label rotation
spine_width	number	0.8	pt	Axis line width

threshold_scatter

fig_atlas.renderers:render_threshold_scatter

Key	Type	Default	Unit	What it does
x_col	text	auto		Column plotted on x
y_col	text	auto		Column plotted on y
effect_col	text	auto		Signed effect column; its sign gives up / down
sig_col	text	auto		Significance column (smaller = stronger, e.g. an adjusted P)
x_transform	one of none, log10, neg_log10	none		Transform of x before plotting
y_transform	one of none, log10, neg_log10	none		Transform of y before plotting
empty_is_missing	true / false	False		Show the missing-data message for an empty table too
missing_text	text	Required columns not found		Message drawn when the columns are missing
missing_text_size	number	auto	pt	Size of the missing-data message (default: title_size)
effect_threshold	number	1.0	effect units	|effect| cut-off for up / down points — raise to call only stronger effects
sig_threshold	number	0.05	significance units	Significance cut-off for up / down points
up_color	colour	#ff0000	hex color	Colour of up points
down_color	colour	#0000ff	hex color	Colour of down points
ns_color	colour	#808080	hex color	Colour of non-significant points
dot_size	number	20	pt^2 (marker area)	Point size — lower for dense plots
ns_alpha	number	0.6	[0-1] opacity	Opacity of non-significant points
sig_alpha	number	0.6	[0-1] opacity	Opacity of up / down points
ns_zorder	number	auto	matplotlib zorder	Drawing order of the ns points (default: matplotlib's)
sig_zorder	number	auto	matplotlib zorder	Drawing order of the up / down points
show_cutoff_lines	true / false	True		Draw the cut-off lines
cutoff_lines	list	auto		Lines to draw: list of {axis: h|v, at: effect|-effect|sig|, width_scale, alpha_scale, style}; 'sig' is the transformed significance cut-off
cutoff_line_color	colour	black	color	Cut-off line colour
cutoff_line_style	text	--		Cut-off line style (matplotlib)
cutoff_line_width	number	1	pt	Cut-off line width
cutoff_line_alpha	number	0.5	[0-1] opacity	Cut-off line opacity
label_mode	one of none, top_n, custom	none		Label points: none, the top_n strongest (|effect| x -log10 significance), or label_custom
label_cols	list	['nearest_gene', 'gene_name', 'symbol', 'gene_id']		Candidate label columns; the first present is used
label_top_n	integer	10	points	Points labelled in top_n mode
label_custom	list	auto		Labels to show in custom mode (matched case-insensitively)
label_size	number	8	pt	Point label size
label_color	colour	black	color	Point label colour
label_box_alpha	number	0.7	[0-1] opacity	Opacity of the box behind labels
label_arrow_color	colour	grey	color	Colour of the label leader lines
label_arrow_width	number	0.5	pt	Width of the label leader lines
label_expand	list	[1.15, 1.4]	multiple of the label box (x, y)	Room adjustText keeps around each label — raise if labels still touch
label_force	list	[0.4, 0.6]	adjustText force (x, y)	How hard labels push apart
label_iter_lim	integer	1000	iterations	Label-placement steps (a fixed count, so every build places the labels the same way) — raise if labels still overlap; lower for a faster build
label_axes_pad_pt	number	2.0	pt	Room kept between a point label and the axes frame (the axis limits widen to make it) — raise if labels still crowd the frame
x_min	number	auto	data coords (after transform)	Lower x limit (both x_min and x_max needed)
x_max	number	auto	data coords (after transform)	Upper x limit
y_min	number	auto	data coords (after transform)	Lower y limit (both y_min and y_max needed)
y_max	number	auto	data coords (after transform)	Upper y limit
grid	true / false	False		Draw a background grid
grid_alpha	number	0.3	[0-1] opacity	Grid opacity
labels_title	text	auto		Panel title
labels_xlabel	text	computed		x-axis title (default: the x column name)
labels_ylabel	text	computed		y-axis title (default: the y column name)
title_size	number	style typography.title_size (else 10)	pt	Panel title font size — lower if the title wraps or crowds the panel
axes_label_size	number	auto	pt	Axis title size (default: rcParams)
tick_label_size	number	auto	pt	Tick label size (default: rcParams)
show_xticklabels	true / false	True		Show x tick labels
show_yticklabels	true / false	True		Show y tick labels
show_legend	true / false	True		Show the up / down / ns legend with counts
legend_position	text	best		Legend anchor (matplotlib loc, or 'outside right')
legend_fontsize	text	computed	pt or matplotlib size name	Legend font size (default: tick_label_size, else 'small')
legend_framealpha	number	auto	[0-1] opacity	Legend frame opacity (default: rcParams)
fit_axes_width	true / false	False		Widen the axes to fill its column, keeping room for the y tick labels
fit_pad_in	number	0.3	inches	Room left of the y tick labels when fitting
fit_left_min	number	0.09	fraction of the column	Smallest left margin when fitting
fit_left_max	number	0.3	fraction of the column	Largest left margin when fitting
fit_right	number	0.98	fraction of the column	Right edge of the axes when fitting

tier_hbar

fig_atlas.renderers:render_tier_hbar

Key	Type	Default	Unit	What it does
category_col	text	category		Column of df with the bar categories (tiers)
count_col	text	count		Column of df with the bar lengths
order	list	auto		Bar order top to bottom (default: order of first appearance)
label_rename_map	mapping	{}		Display label per category
bar_colors	mapping	{}	hex color per category	Colour per category
default_bar_color	colour	#3b73b9	hex color	Colour of categories without one
show_value_labels	true / false	True		Print each bar's count at its end
value_label_fontsize	number	computed	pt	Count label size (default axes_label_size)
value_label_offset	number	0.015	fraction of x range	Gap between bar end and its count — raise if labels touch the bars
xlim	list	auto	data coords [min, max]	x range; only the max is used
xlim_headroom	number	1.12	x the largest count	x range when xlim is unset — raise if value labels clip at the right
xlabel	text	n genes		x-axis title
labels_title	text	Final target genes by tier		Panel title
title_size	number	13	pt	Panel title font size
axes_label_size	number	11	pt	Axis title font size
tick_label_size	number	8	pt	Tick label font size

treatment_schematic

fig_atlas.renderers:render_treatment_schematic

Key	Type	Default	Unit	What it does
xlim	list	[-1, 76]	hours [min, max]	x range of the timeline axes
ylim	list	[-2.5, 5.2]	data coords [min, max]	y range shared by both axes
regimen_labels	list	[{'text': 'Acute', 'x': 0.75, 'y': 1.5, 'fontsize': 14.0, 'fontweight': 'bold', 'color': '#0F172A'}, {'text': 'Chronic', 'x': 0.75, 'y': 3.3, 'fontsize': 14.0, 'fontweight': 'bold', 'color': '#0F172A', 'bracket': {'draw': True, 'y_top': 3.9, 'y_bot': 2.7, 'x_tip': 0.95, 'x_corner': 0.88, 'x_stem': 0.82, 'color': '#475569', 'lw': 1.8}}]		Regimen names left of the bars: text, x/y (axes data coords), fontsize (pt), colour, optional bracket
label_fontsize	number	13.0	pt	Default size of the regimen labels
timeline_range	list	[0, 74]	hours [start, end]	Extent of the timeline line
timeline_ticks	list	[0, 3, 24, 48, 72]	hours	Tick positions on the timeline
timeline_labels	list	['0', '3', '24', '48', '72']		Tick labels
timeline_linewidth	number	3.2	pt	Timeline line width
y_axis	number	0.2	data coords	Height of the timeline line — lower to move it away from the bars
tick_len	number	0.4	data coords	Tick length on the timeline
tick_fontsize	number	15.0	pt	Timeline tick label size
tick_label_offset	number	0.75	data coords	Gap between timeline and its tick labels
treatment_bars	list	[{'start': 0, 'end': 3, 'y': 1.5}, {'start': 0, 'end': 24, 'y': 2.7}, {'start': 0, 'end': 48, 'y': 3.9}]	hours (start, end) and data coords (y)	One exposure bar per regimen
bar_color	colour	#FF0000	hex color	Exposure bar fill
bar_edgecolor	colour	#000000	hex color	Exposure bar outline
bar_height	number	0.56	data coords	Exposure bar thickness
bar_linewidth	number	2.4	pt	Exposure bar outline width
samplings	list	[{'x': 24, 'y': 1.5, 'label': '1D'}, {'x': 72, 'y': 1.5, 'label': '3D'}, {'x': 72, 'y': 2.7, 'label': '24H'}, {'x': 72, 'y': 3.9, 'label': '48H'}]	hours (x) and data coords (y)	Sampling time points (circle per sample, with label)
color_rna	colour	#8CE04F	hex color	Fill of the RNA-seq half of a sampling circle
color_atac	colour	#00C5FF	hex color	Ring colour marking ATAC-seq
circle_size	number	1700	pt^2 (marker area)	Sampling circle size
circle_linewidth	number	3.5	pt	Sampling circle ring width
legend	mapping	{}		Legend layout: y, bar_x, bar_w, bar_label_x, bar_height, circle_size, circle_linewidth, rna_x, rna_label_x, rna_edgecolor, atac_x, atac_label_x, atac_circle_linewidth
y_legend	number	-1.8	data coords	Legend row height (legend.y takes precedence)
legend_fontsize	number	14.5	pt	Legend text size

ts_profile

fig_atlas.renderers:render_ts_profile

Key	Type	Default	Unit	What it does
sample_groups	mapping	auto		Group name -> sample columns, for dividers and group labels
profile_show_group_labels	true / false	True		Label each sample group above the profile
profile_group_divider_color	colour	#999999	hex color	Colour of the lines between groups
profile_line_color	colour	#f39c12	hex color	Colour of the per-gene lines
profile_line_width	number	0.6	pt	Per-gene line width
profile_line_alpha	number	0.25	alpha [0-1]	Per-gene line opacity — lower when many genes are drawn
profile_mean_line_color	colour	#c0392b	hex color	Colour of the mean line
profile_mean_line_width	number	2.0	pt	Mean line width
profile_grid	true / false	True		Draw a background grid
profile_y_min	number	computed	data coords	Lower y limit (default z_min, else data)
profile_y_max	number	computed	data coords	Upper y limit (default z_max, else data)
z_min	number	auto	z-score	Shared lower limit, used when profile_y_min is not set
z_max	number	auto	z-score	Shared upper limit, used when profile_y_max is not set
profile_labels_title	text	auto		Panel title
profile_labels_ylabel	text	Z-score		y-axis title
title_size	number	13	pt	Panel title font size
axes_label_size	number	11	pt	Axis title font size
tick_label_size	number	8	pt	Tick label font size

two_set_euler

fig_atlas.renderers:render_two_set_euler

Key	Type	Default	Unit	What it does
a_label	text	A		Name of set A, printed above its circle with n
b_label	text	B		Name of set B, printed above its circle with n
a_color	colour	#93c5fd	hex color	Fill of the A-only region
b_color	colour	#fcd34d	hex color	Fill of the B-only region
both_color	colour	#2563eb	hex color	Fill of the intersection
fill_alpha	number	0.55	[0-1] opacity	Opacity of the circle fills
edge_color	colour	#334155	hex color	Circle outline colour (and the outside count text)
edge_width	number	0.6	pt	Circle outline width
frame_color	colour	#94a3b8	hex color	Colour of the surrounding 'all genes' box
frame_width	number	0.6	pt	Width of the surrounding box
frame_pad	number	0.12	x the larger radius	Gap between circles and the box sides
frame_top_room	number	0.55	x the larger radius	Room above the circles for the set labels — raise if set labels touch the box
frame_bottom_room	number	0.3	x the larger radius	Room below the circles for the totals
count_fontsize	number	6.0	pt	Region count size
label_fontsize	number	6.0	pt	Set label size
both_label	text	linked		Word above the intersection count
both_note	text	auto		Extra line in the intersection (e.g. 'core 41')
both_text_color	colour	white	color	Text colour inside the intersection
neither_label	text	neither		Label of the genes outside both circles
total_label	text	all genes		Label of the total
min_region_frac	number	0.28	x the larger radius	A region narrower than this gets its count outside
both_min_width_frac	number	0.45	x the larger radius	A lens narrower than this gets its label outside the circles
both_outside_offset	list	[0.35, 0.45]	[dx, dy] in radii	Position of the outside intersection label
both_outside_color	colour	#1e3a8a	hex color	Colour of the outside intersection label
labels_title	text	auto		Panel title (none = no title)
title_size	number	8.0	pt	Panel title font size
title_pad	number	4	pt	Gap between title and diagram

venn

fig_atlas.renderers:render_venn

Key	Type	Default	Unit	What it does
set_labels	list	[]		Sets to draw (2 or 3): values of the long table's dataset column
display_labels	list	[]		Names printed for the sets (default: set_labels)
unit	text	Gene		What is counted, used in the title (e.g. Gene, Peak)
filter_name	text	All Genes		Name of the filter, used in the title
title_size	number	12	pt	Panel title font size

violin

fig_atlas.renderers:render_violin

Key	Type	Default	Unit	What it does
y_log	true / false	False		Log-scaled y axis
y_min	number	auto	data coords	Lower y limit (both y_min and y_max needed)
y_max	number	auto	data coords	Upper y limit
grid	true / false	False		Draw horizontal grid lines
grid_alpha	number	0.3	[0-1] opacity	Grid opacity
spine_width	number	auto	pt	Axis line width (default: rcParams)
hide_top_right	true / false	True		Hide the top and right axis lines
labels_title	text	auto		Panel title (none: no title)
labels_xlabel	text	computed		x-axis title (default: the x column's name)
labels_ylabel	text	computed		y-axis title (default: the y column's name)
title_size	number	8.0	pt	Panel title size
axes_label_size	number	auto	pt	Axis title size (default: rcParams)
tick_label_size	number	auto	pt	Tick label size (default: rcParams)
show_legend	true / false	True		Show the group legend (only with a group_col)
legend_loc	text	best		Legend location (matplotlib loc)
legend_fontsize	number	auto	pt	Legend font size (none: tick_label_size)
legend_frameon	true / false	False		Draw a frame around the legend
x_col	text	group		Column with the categories (x axis)
y_col	text	value		Column with the values
x_order	list	auto		Category order on x (default: order in the data)
x_labels	mapping	{}		Shown name per category (default: the category)
group_colors	mapping	{}	hex color	Fill colour per category (default: matplotlib colour cycle)
violin_width	number	0.8	x units (categories are 1 apart)	Width of each violin — lower for more space between categories
violin_alpha	number	0.6	[0-1] opacity	Violin fill opacity
violin_edge_color	colour	#374151	hex color	Violin outline colour
violin_edge_width	number	0.6	pt	Violin outline width
bandwidth	number	auto	fraction of the data's spread (scipy gaussian_kde bw_method)	Smoothing of the violin outline (default: Scott's rule) — lower to follow the data more closely, raise for a smoother outline
show_quartiles	true / false	True		Draw the median (dot) and quartiles (thick line) inside each violin
median_color	colour	#ffffff	hex color	Median dot colour
median_size	number	12.0	pt^2 (marker area)	Median dot size
quartile_color	colour	#111827	hex color	Quartile bar colour
quartile_width	number	3.0	pt	Quartile bar width
show_points	true / false	False		Overlay every value as a point
point_color	colour	#111827	hex color	Point colour
point_size	number	6.0	pt^2 (marker area)	Point size
point_alpha	number	0.6	[0-1] opacity	Point opacity
point_edge_width	number	0.0	pt	Point outline width (0: none)
point_jitter	number	0.08	x units	Horizontal scatter of the points
point_seed	integer	0	random seed	Seed of the jitter (fixed for reproducible output)

volcano

fig_atlas_omics.renderers:render_volcano

Key	Type	Default	Unit	What it does
log2fc_threshold	number	1.0	log2 fold change	|log2FC| cut-off for up / down points — raise to call only stronger changes
padj_threshold	number	0.05	adjusted P	padj cut-off for up / down points
up_color	colour	#ff0000	hex color	Colour of up-regulated points
down_color	colour	#0000ff	hex color	Colour of down-regulated points
ns_color	colour	#808080	hex color	Colour of non-significant points
dot_size	number	20	pt^2 (marker area)	Point size — lower for dense plots
show_cutoff_lines	true / false	True		Draw the dashed cut-off lines
cutoff_line_color	colour	black	color	Cut-off line colour
cutoff_line_style	text	--		Cut-off line style (matplotlib)
cutoff_line_width	number	1	pt	Cut-off line width
cutoff_line_alpha	number	0.5	[0-1] opacity	Cut-off line opacity
annotation_mode	one of none, top_n, custom	none		Label genes: none, the top_n strongest (|log2FC| x -log10 padj), or annotation_custom_genes
annotation_top_n	integer	10	genes	Genes labelled in top_n mode
annotation_custom_genes	list	auto		Genes labelled in custom mode (matched case-insensitively)
annotation_label_size	integer	8	pt	Gene label size
annotation_iter_lim	integer	1000	iterations	Label-placement steps (a fixed count, so every build places the labels the same way) — raise if labels still overlap; lower for a faster build
x_min	number	auto	log2 fold change	Lower x limit (both x_min and x_max needed)
x_max	number	auto	log2 fold change	Upper x limit
y_min	number	auto	-log10 padj	Lower y limit (both y_min and y_max needed)
y_max	number	auto	-log10 padj	Upper y limit
labels_title	text	auto		Panel title
labels_xlabel	text	Log2 Fold Change		x-axis title
labels_ylabel	text	-Log10(Padj)		y-axis title
title_size	number	10	pt	Panel title font size
show_xticklabels	true / false	True		Show x tick labels
show_yticklabels	true / false	True		Show y tick labels
show_legend	true / false	True		Show the up / down / ns legend
legend_position	text	best		Legend anchor (matplotlib loc)

Recipes

A recipe is a core shape with a field's defaults and parameter names; fig_atlas.render("<name>", ...) draws it.

Recipe	Renderer	Defaults
ma_plot	fig_atlas.renderers.threshold_scatter:render_threshold_scatter	axes_label_size: 11, cutoff_lines: [{'axis': 'h', 'at': 0}, {'axis': 'h', 'at': 'effect', 'width_scale': 0.6, 'alpha_scale': 0.7, 'style': ':'}, {'axis': 'h', 'at': '-effect', 'width_scale': 0.6, 'alpha_scale': 0.7, 'style': ':'}], dot_size: 10, effect_col: log2FoldChange, effect_threshold: 0.585, empty_is_missing: True, labels_title: MA Plot, labels_xlabel: log10(Mean Accessibility), labels_ylabel: Log2 Fold Change, legend_framealpha: 0.9, missing_text: No data to display, ns_alpha: 0.5, ns_zorder: 2, sig_alpha: 1.0, sig_col: padj, sig_zorder: 3, tick_label_size: 8, title_size: 13, x_col: baseMean, x_transform: log10, y_col: log2FoldChange
volcano	fig_atlas.renderers.threshold_scatter:render_threshold_scatter	cutoff_lines: [{'axis': 'h', 'at': 'sig'}, {'axis': 'v', 'at': 'effect'}, {'axis': 'v', 'at': '-effect'}], effect_col: log2FC, fit_axes_width: True, grid: True, labels_xlabel: Log2 Fold Change, labels_ylabel: -Log10(Padj), legend_fontsize: small, missing_text: Required columns not found: log2FC and padj, missing_text_size: 14, ns_alpha: 0.6, sig_alpha: 0.6, sig_col: padj, x_col: log2FC, y_col: padj, y_transform: neg_log10