Can plot barplot of NES of pathways from one GSEA result, or compare NES for chosen pathways between two GSEA results.
Usage
plot_GSEA_barplot(
gsea_res,
gsea_name = "GSEA",
gsea_pws = NULL,
n_pws = 5,
pw_format = FALSE,
pw_split = FALSE,
pw_source = TRUE,
pw_ignore = NULL,
pw_size = 5,
gsea2_res = NULL,
gsea2_name = NULL,
order2 = FALSE,
ptrn2 = "none",
NES_cutoff = NULL,
sig_cutoff = NULL,
colors = c("firebrick", "darkblue"),
title = NULL,
savename = NULL,
width = 10,
height = NULL
)Arguments
- gsea_res
df/string; (path to) GSEA results w/
pathwayandNEScolumns- gsea_name
string; description of GSEA results
- gsea_pws
char vector; pathways in GSEA results to plot
- n_pws
integer; if no pathways provided, top/bottom n pathways (ordered by NES) to plot
- pw_format
logical; clean up pathway names?
- pw_split
logical; T to split pathway names into multiple lines
- pw_source
logical; T to append pathway source in parenthesis
- pw_ignore
char vector; list of terms to ignore for name formatting
- pw_size
numeric; pathway name text size
- gsea2_res
df/string; (path to) 2nd GSEA results w/
pathwayandNEScolumns- gsea2_name
string; description of 2nd GSEA results
- order2
logical; order pathways by NES of 2nd GSEA results?
- ptrn2
string;
ggpatternpattern arg: 'stripe', 'crosshatch', 'point', 'circle', 'none'- NES_cutoff
numeric; value to draw NES cutoff line at
- sig_cutoff
vector;
sig_cutoff[1]is colname of significance values ("pval" or "padj"),sig_cutoff[2]is numeric cutoff value: if higher than this value, alpha will be 0.5. Ex.sig_cutoff = c("pval", 0.05)orsig_cutoff = c("padj", 0.1)- colors
vector;
colors[1]for positive bar color,colors[2]for negative bar color- title
string; plot title
- savename
string; file path to save plot under
- width
numeric; plot width
- height
numeric; plot height