comparegsea_scatter: Generate a scatter plot comparing two gene set enrichment...

In SCdeconR: Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq Data as Reference

Generate a scatter plot comparing two gene set enrichment analysis results

Description

Generate a scatter plot of normalized enrichment scores comparing two results for gene set enrichment analysis, e.g. w/wo adjusting for cell proportion differences.

Usage

comparegsea_scatter(
  gseares_path1,
  gseares_path2,
  result_names = NULL,
  nes_cutoff = 2,
  pval_cutoff = 0.1,
  pvalflag = TRUE,
  interactive = FALSE
)

Arguments

gseares_path1	path to GSEA output.
gseares_path2	path to a second GSEA output.
result_names	a vector of length 2 indicating the names of the two GSEA results. If NULL, names will be set to c("results1", "results2")
nes_cutoff	normalized enrichment score cutoff to identify enriched gene-sets.
pval_cutoff	p value cutoff to identify enriched gene-sets.
pvalflag	a logical value indicating whether to use adjusted p value in selecting enriched gene-sets. Default to TRUE.
interactive	a logical value indicating whether to generate an interactive plot. Default to FALSE.

Details

this function does not support output from GSEA R implementation

Value

a ggplot object or plotly object if interactive is set to TRUE

SCdeconR documentation built on May 29, 2024, 9:03 a.m.