If subtitle is not specified, Kolmogorov-Smirnov enrichment p-value is calculated to check if the genes in the pathway separate from the genes not in the chosen pathway based on ranking by the desired rankcol.
Usage
plot_GSEA_pathway(
sig,
geneset,
genecol = "gene",
rankcol,
rankcol_name = rankcol,
hightolow = FALSE,
label = length(geneset) < 20,
legendpos = "none",
hl_color = "firebrick3",
lab_high = NULL,
lab_low = NULL,
hllab = "Highlight",
title = NULL,
subtitle = NULL,
savename = NULL
)Arguments
- sig
df/string; (path to) dataframe with genecol + rankcol columns
- geneset
vector; list of genes
- genecol
string; colname of gene names in
sig- rankcol
string; colname of values in
sig- rankcol_name
string; descriptive name of values
- hightolow
logical; T for high values on left, low on right
- label
logical; T to label highlighted genes
- legendpos
vector; value btwn 0-1 as legend coordinates (ggplot2 legend.position)
- hl_color
string; color for highlight
- lab_high
string; description of high values
- lab_low
string; description of low values
- hllab
string; description of highlighted values
- title
string; plot title
- subtitle
string; plot subtitle; !! overwrites p-val_enrichment
- savename
string; filepath to save png under
Examples
airway_deseq = Rubrary::airway_deseq_res
genes = Rubrary::GSEA_pathways$GOBP_REGULATION_OF_GLUCOSE_IMPORT
Rubrary::plot_GSEA_pathway(
sig = airway_deseq,
geneset = genes,
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",
hllab = "Highlight genes",
title = "Airway Treated vs. Untreated DESeq - Glucose Import Regulation Genes"
)
