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Plot transcription factor activity

Source: R/DorotheaPlot.R
DorotheaPlot.Rd

Visualize TF activity stored by RunDorothea(). Comparison plots ("bar", "lollipop", "volcano") test two groups and show the mean activity difference group1 - group2. "dim" compares TF activity with TF expression on embeddings, and "targets" shows a regulon-target volcano for one TF. Use GroupHeatmap, FeatureStatPlot, and FeatureDimPlot directly for ordinary activity visualizations.

Usage

DorotheaPlot(
  object,
  group.by,
  group1 = NULL,
  group2 = NULL,
  plot_type = c("bar", "lollipop", "volcano", "dim", "targets"),
  tool_name = "Dorothea",
  assay_name = NULL,
  features = NULL,
  top_n = 30,
  test.use = c("wilcox.test", "t.test"),
  p.adjust.method = "BH",
  color.by = c("p_val", "p_val_adj"),
  rank.by = c("abs_logFC", "p_val", "p_val_adj", "logFC"),
  sort.by = c("logFC", "abs_logFC", "p_val", "p_val_adj"),
  p_floor = .Machine$double.xmin,
  padjustCutoff = 0.05,
  palette = "RdBu",
  palcolor = NULL,
  dim_args = list(),
  compare_expression = TRUE,
  expression_assay = NULL,
  expression_layer = "data",
  nlabel = 10,
  reduction = NULL,
  bar_width = 0.72,
  pt.size = 3.2,
  point_size = NULL,
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  fill.title = NULL,
  flip = TRUE,
  cols = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  return_data = FALSE,
  verbose = TRUE,
  srt = NULL
)

Arguments

object

A Seurat object containing results from RunDorothea().

group.by

Metadata column used to define groups.

group1, group2

Two group labels to compare. Required for "bar", "lollipop", "volcano", and "targets". Positive logFC means higher TF activity (or target expression) in group1. Ignored for "dim".

plot_type

Plot type. "bar" and "lollipop" show signed activity differences, "volcano" shows TF-level significance versus logFC, "dim" compares activity and expression on embeddings, and "targets" shows a regulon-target volcano.

tool_name

Name of the srt@tools entry created by RunDorothea().

assay_name

Activity assay used for "dim". If NULL, the assay stored by RunDorothea() is used, or "dorothea".

features

TFs to plot. If NULL, "bar"/"lollipop" use the top top_n TFs, "volcano" shows all tested TFs, "dim" uses TFs present in both activity and expression assays, and "targets" uses the TF with the largest absolute activity difference.

top_n

Number of TFs to show when features = NULL. Ignored for "volcano", which always plots every tested TF. Set NULL to show all tested TFs in other comparison plots.

test.use

Statistical test used for each TF or target gene in comparison plots.

p.adjust.method

Method passed to stats::p.adjust.

color.by

P-value column used for comparison-plot color scales.

rank.by

Metric used to select top TFs when features = NULL in comparison plots.

sort.by

Metric used to order TFs in "bar" and "lollipop" plots.

p_floor

Lower bound used before -log10() transformation.

padjustCutoff

Adjusted p-value cutoff used to mark significant TFs in "volcano" plots and non-supporting targets in "targets" plots.

palette, palcolor

Palette passed to palette_colors() for comparison plots.

dim_args

Additional arguments passed to FeatureDimPlot() when plot_type = "dim".

compare_expression

Whether "dim" also plots TF gene expression beside TF activity.

expression_assay, expression_layer

Assay and layer used for TF expression in "dim" and for target genes in "targets".

nlabel

Number of significant TFs labeled in "volcano" plots, or significant target genes labeled in "targets" plots.

reduction

Reduction used by "dim" plots. If NULL, the default reduction of object is used.

bar_width

Width of bars in "bar" plots.

pt.size

Point size in "lollipop", "volcano", and "targets" plots.

point_size

Deprecated alias(es) for pt.size; supply exactly one of the two. It will be removed in scop 1.0.0.

aspect.ratio

Panel aspect ratio.

legend.position

Legend placement ("none", "left", "right", "bottom", "top"), direction, and title. legend.title = NULL uses the group name.

legend.direction

Legend direction: "horizontal" or "vertical".

title, xlab, ylab, fill.title

Axis, plot, and legend titles.

flip

Whether to draw comparison bar/lollipop plots horizontally.

cols

Optional three-color vector used instead of palette for diverging comparison scales. Kept for backward compatibility.

theme_use, theme_args

Theme name or function, plus extra theme arguments.

return_data

Whether to return a list with the plot and statistics.

verbose

Whether to print the message. Default is TRUE.

srt

Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A ggplot or patchwork object, or a list with plot and data when return_data = TRUE.

See also

RunDorothea, GroupHeatmap, FeatureDimPlot, FeatureStatPlot

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub, verbose = FALSE)
#> ℹ [2026-11-12 05:11:30] Skip `log1p()` because `layer = data` is not "counts"
pancreas_sub <- RunDorothea(
  pancreas_sub,
  layer = "counts",
  species = "Mus_musculus",
  method = "ulm",
  minsize = 5
)
#> ℹ [2026-11-12 05:11:37] Run "DoRothEA"/decoupleR with 12895 regulon edges
#> ℹ [2026-11-12 05:11:48] "DoRothEA" TF activity scores stored in assay "dorothea"
#> ℹ [2026-11-12 05:11:48] "DoRothEA" TF activity scores stored in <Seurat> metadata

DorotheaPlot(
  pancreas_sub,
  group.by = "CellType",
  group1 = "Endocrine",
  group2 = "Ductal",
  plot_type = "bar",
  top_n = 20
)
#> ℹ [2026-11-12 05:11:48] Compare "DoRothEA" TF activity: "Endocrine" vs "Ductal"


DorotheaPlot(
  pancreas_sub,
  group.by = "CellType",
  group1 = "Endocrine",
  group2 = "Ductal",
  plot_type = "lollipop",
  top_n = 20
)
#> ℹ [2026-11-12 05:11:49] Compare "DoRothEA" TF activity: "Endocrine" vs "Ductal"


DorotheaPlot(
  pancreas_sub,
  group.by = "CellType",
  group1 = "Endocrine",
  group2 = "Ductal",
  plot_type = "volcano"
)
#> ℹ [2026-11-12 05:11:50] Compare "DoRothEA" TF activity: "Endocrine" vs "Ductal"


tfs <- head(rownames(pancreas_sub[["dorothea"]]), 20)
GroupHeatmap(
  pancreas_sub,
  group.by = "CellType",
  features = tfs,
  assay = "dorothea",
  layer = "data",
  exp_method = "raw",
  lib_normalize = FALSE
)$plot


DorotheaPlot(
  pancreas_sub,
  group.by = "CellType",
  features = "Sox9",
  plot_type = "dim"
)
#> ℹ [2026-11-12 05:11:51] Draw "DoRothEA" embedding plots for 1 TFs


FeatureStatPlot(
  pancreas_sub,
  group.by = "CellType",
  stat.by = c("Sox9", "Neurod1", "Pdx1"),
  assay = "dorothea",
  layer = "data",
  plot_type = "violin"
)

FeatureDimPlot(
  pancreas_sub,
  features = c("Sox9", "Neurod1", "Pdx1"),
  assay = "dorothea",
  layer = "data"
)


DorotheaPlot(
  pancreas_sub,
  group.by = "CellType",
  group1 = "Endocrine",
  group2 = "Ductal",
  features = "Sox9",
  plot_type = "targets"
)
#> ! [2026-11-12 05:11:53] Dropping 3 "Sox9" targets missing from assay "RNA"
#> ℹ [2026-11-12 05:11:53] Draw "DoRothEA" regulon-target volcano for "Sox9" (10 targets)