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plot_GSEA_pathway that works nicely with lapply

Source: R/plot_GSEA_pathway.R
plot_GSEA_batch.Rd

plot_GSEA_pathway that works nicely with lapply

Usage

plot_GSEA_batch(
  path_name,
  pthwys,
  sig,
  genecol = "gene",
  rankcol,
  rankcol_name = rankcol,
  hllab = "Pathway genes",
  hightolow = FALSE,
  lab_low = NULL,
  lab_high = NULL,
  legendpos = c(0.5, 0.2),
  label = length(pthwys[[path_name]]) < 50,
  sig_name = "",
  savedir = NULL
)

Arguments

path_name

string; name of pathway

pthwys

named list; key = geneset name, values = char vector of genes in geneset

sig

dataframe; signature

genecol

string; colname of gene names in sig

rankcol

string; colname of values to rank by

rankcol_name

string; descriptor of rankcol

hllab

string; descriptor of highlighted genes

hightolow

logical; T for high values on left, low on right

lab_low

string; label for low rankcol values

lab_high

string; label for high rankcol values

legendpos

vector; value btwn 0-1 as legend coordinates (ggplot2 legend.position)

label

logical; T to label points in plot

sig_name

string; name of signature

savedir

string; directory path for saving plot

Value

Gene set enrichment plot as ggplot object