Plot scFEA metabolite balance changes

Usage

scFEABalanceBarPlot(
  object,
  group.by,
  ident.1 = NULL,
  ident.2 = NULL,
  assay = "scFEAbalance",
  layer = "data",
  top_n = NULL,
  p_adj_cutoff = 0.01,
  palcolor = c("#D73027", "#4575B4"),
  title = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  srt = NULL
)

Arguments

object: 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. Difference is `mean(ident.1) - mean(ident.2)`. If both are `NULL`, one-vs-rest contrasts are generated automatically.
assay: Balance assay name.
layer: Balance assay layer.
top_n: If `NULL`, plot all metabolites. If positive, plot the top `top_n` increased and top `top_n` decreased metabolites after the adjusted-p-value filter.
p_adj_cutoff: Adjusted p-value cutoff used when `top_n` is not `NULL`.
palcolor: Two colors for the higher and lower group.
title: Optional plot title.
theme_use, theme_args: Theme name or function, plus extra theme arguments.
srt: Deprecated alias for `object`; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

For a single contrast, a list with `plot` and plotted `data`. 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.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
pancreas_sub <- RunscFEA(pancreas_sub, group.by = "SubCellType")
scFEABalanceBarPlot(pancreas_sub, group.by = "SubCellType", ident.1 = "Alpha", ident.2 = "Beta")
} # }