plot_enrichment {GWENA} | R Documentation |
Wrapper of the gprofiler2::gostplot function. Adding support of colorblind palet and selection of subsets if initial multiple query, and/or sources to plot.
plot_enrichment( enrich_output, modules = "all", sources = "all", colorblind = TRUE, custom_palette = NULL, ... )
enrich_output |
list, bio_enrich result which are in fact gprofiler2::gost output. |
modules |
string or vector of characters designing the modules to plot. "all" by default to plot every module. |
sources |
string or vector of characters designing the sources to plot. "all" by default to plot every source. |
colorblind |
boolean, indicates if a colorblind friendly palette should be used. |
custom_palette |
vector of character, colors to be used for plotting. |
... |
any other parameter you can provide to gprofiler2::gostplot. |
Note: The colorblind friendly palette is limited to maximum 8 colors, therefore 8 sources of enrichment.
A plotly object representing enrichment for specified modules
custom_path <- system.file("extdata", "h.all.v6.2.symbols.gmt", package = "GWENA", mustWork = TRUE) multi_module <- list(mod1 = c("BIRC3", "PMAIP1", "CASP8", "JUN", "BCL2L11", "MCL1", "IL1B", "SPTAN1", "DIABLO", "BAX", "BIK", "IL1A", "BID", "CDKN1A", "GADD45A"), mod2 = c("TAF1C", "TARBP2", "POLH", "CETN2", "POLD1", "CANT1", "PDE4B", "DGCR8", "RAD51", "SURF1", "PNP", "ADA", "NME3", "GTF3C5", "NT5C")) multi_module_enriched <- bio_enrich(multi_module, custom_path) plot_enrichment(multi_module_enriched)