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Plot differential DoRothEA TF activity

Source: R/RunDorothea.R
DorotheaPlot.Rd

Compare DoRothEA transcription factor activity between two groups and draw a signed bar plot. Bar height is the mean activity difference group1 - group2; fill color is the signed -log10(p) or -log10(adjusted p), where the sign follows the activity difference.

Usage

DorotheaPlot(
  srt,
  group.by,
  group1,
  group2,
  tool_name = "Dorothea",
  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,
  bar_width = 0.85,
  cols = c("#2166AC", "white", "#B2182B"),
  title = NULL,
  xlab = NULL,
  ylab = "logFC",
  fill.title = NULL,
  angle = 90,
  hjust = 1,
  vjust = 0.5,
  theme_use = "theme_scop",
  theme_args = list(),
  return_data = FALSE,
  verbose = TRUE
)

Arguments

srt

A Seurat object containing results from RunDorothea().

group.by

Metadata column used to define groups.

group1, group2

Two group labels to compare. Positive logFC means higher TF activity in group1.

tool_name

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

features

TFs to plot. If NULL, all TFs are tested and the top top_n TFs are shown.

top_n

Number of TFs to show when features = NULL. Set NULL to show all tested TFs.

test.use

Statistical test used for each TF.

p.adjust.method

Method passed to stats::p.adjust.

color.by

P-value column used for bar fill.

rank.by

Metric used to select top TFs when features = NULL.

sort.by

Metric used to order TFs on the x-axis.

p_floor

Lower bound used before -log10() transformation.

bar_width

Width of bars.

cols

Color vector of length 3 for low, midpoint, and high values.

title, xlab, ylab, fill.title

Axis, plot, and legend titles.

angle

X-axis text angle.

hjust, vjust

X-axis text justification.

theme_use

Theme function used to style the plot.

theme_args

Other arguments passed to theme_use.

return_data

Whether to return a list with the plot and statistics.

verbose

Whether to print the message. Default is TRUE.

Value

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

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub, verbose = FALSE)
pancreas_sub <- RunDorothea(
  pancreas_sub,
  layer = "counts",
  species = "Mus_musculus",
  method = "ulm",
  minsize = 5,
  new_assay = FALSE
)
groups <- unique(as.character(pancreas_sub$CellType))
DorotheaPlot(
  pancreas_sub,
  group.by = "CellType",
  group1 = groups[1],
  group2 = groups[2]
)