Plot scFEA flux Cohen's d volcano plots

Plot scFEA flux Cohen's d volcano plots

Usage

scFEAVolcanoPlot(
  srt,
  group.by,
  ident.1 = NULL,
  ident.2 = NULL,
  assay = "scFEAflux",
  layer = "data",
  label_by = c("reaction", "module", "module_reaction"),
  pathways = NULL,
  p_adj_cutoff = 0.001,
  cohen_cutoff = 0.2,
  combine = TRUE,
  width = 12,
  height = 10.4,
  verbose = TRUE
)

Arguments

srt

A Seurat object returned by [RunscFEA()].

group.by

Metadata column defining groups. If `ident.1` and `ident.2` are both `NULL`, each group is compared against all remaining cells.

ident.1, ident.2

Group names to compare. Cohen's d is `mean(ident.1) - mean(ident.2)` divided by pooled standard deviation. If both are `NULL`, one-vs-rest contrasts are generated automatically.

assay

Flux assay name.

layer

Flux assay layer.

label_by

Label mode for significant pathway modules.

pathways

Optional `SM_anno` classes to plot.

p_adj_cutoff

Adjusted p-value cutoff for highlighting, labels, and the horizontal threshold line.

cohen_cutoff

Absolute Cohen's d cutoff for highlighting, labels, and the vertical threshold lines.

combine

Whether to combine pathway plots into 2 x 2 paged panels. If `FALSE`, returns one plot per pathway.

width, height

Suggested export size. Stored as attributes on the returned plot object.

verbose

Whether to print messages.

Value

For a single contrast, a paged list of `ggplot` objects when `combine = TRUE`, otherwise a named list of pathway `ggplot` objects. Statistics are stored in the `"data"` attribute. For automatic one-vs-rest mode, a named list of single-contrast results is returned and combined statistics are stored in the outer `"data"` attribute.