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Plot scFEA metabolite balance changes

Source: R/RunscFEA.R
scFEABalanceBarPlot.Rd

Plot scFEA metabolite balance changes

Usage

scFEABalanceBarPlot(
  srt,
  group.by,
  ident.1 = NULL,
  ident.2 = NULL,
  assay = "scFEAbalance",
  layer = "data",
  top_n = NULL,
  p_adj_cutoff = 0.01,
  title = NULL
)

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. 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`.

title

Optional plot title.

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.