plot_GSEA_pathway wrapper that works nicely with lapply

plot_GSEA_pathway wrapper that works nicely with lapply

Usage

plot_GSEA_pathway_batch(
  path_name,
  pthwys,
  sig,
  genecol = "gene",
  rankcol,
  rankcol_name = rankcol,
  hllab = "Pathway genes",
  hightolow = FALSE,
  format_name = TRUE,
  ignore_name = NULL,
  lab_low = NULL,
  lab_high = NULL,
  legendpos = c(0.5, 0.2),
  hl_color = "firebrick3",
  label = length(pthwys[[path_name]]) < 50,
  savedir = NULL,
  sig_name = ""
)

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

format_name

logical; T to run pathway name through Rubrary::format_GSEA_name

ignore_name

char vector; phrases to exclude title case for in Rubrary::format_GSEA_name

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)

hl_color

string; color for highlight

label

logical; T to label points in plot

savedir

string; directory path for saving plot

sig_name

string; name of signature to append to save path

Value

Gene set enrichment plot as ggplot object

Examples

airway_deseq = Rubrary::airway_deseq_res
pathways <- Rubrary::GSEA_pathways
pws_plot <- c("HALLMARK_ADIPOGENESIS", "GOCC_POSTSYNAPTIC_MEMBRANE")
lapply(
  pws_plot,
  Rubrary::plot_GSEA_pathway_batch,
  pthwys = pathways,
  sig = airway_deseq,
  genecol = "hgnc_symbol",
  rankcol = "sign_log_p",
  rankcol_name = "Sign log p value",
  lab_high = "\U2191 in treated\n\U2193 in untreated",
  lab_low = "\U2191 in untreated\n\U2193 in treated",
)
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