plot_FRmatch: Plotting function for FR-Match results

In JCVenterInstitute/FRmatch: Cell type matching in single-cell RNA-sequencing data using FR-Match

Plotting function for FR-Match results

Description

This function takes in the FRmatch output and generates plots for the matching results.

Usage

plot_FRmatch(
  rst.FRmatch,
  type = "matches",
  p.adj.method = "BY",
  sig.level = 0.05,
  reorder = TRUE,
  ignore.unassigned = FALSE,
  return.value = FALSE,
  cellwidth = 10,
  cellheight = 10,
  main = NULL,
  filename = NA,
  ...
)

Arguments

rst.FRmatch	The FRmatch output.
type	If type="matches" (default), it plots the one-way matches. If type="padj", it plots the distribution of adjusted p-values.
p.adj.method	P-value adjustment method for multiple hypothesis testing correction. Default: "BY". For more options, please see p.adjust.methods.
sig.level	Numeric variable that specifies the significance level of adjusted p-value. A MATCH is >sig.level. Default: 0.05.
reorder	Boolean variable indicating if to reorder the columns so that matches are aligned along the diagonal. It improves the interpretability of the one-way match plot. Default: TRUE.
ignore.unassigned	Boolean variable indicating if to skip the columns of unassigned query clusters in the type="matches" plot. Default: FALSE. If TRUE, number of ignored columns reported in the unassigned row.
return.value	Boolean variable indicating if to return the plotted values. Default: FALSE.
cellwidth, cellheight, main, filename, ...	Plotting parameters passed to hist.

Value

If return.value = TRUE, a matrix of one-way matching values 1 = match, and 0 = no match, or a matrix of adjusted p-values.

See Also

plot_bi_FRmatch.

JCVenterInstitute/FRmatch documentation built on June 11, 2025, 12:28 a.m.