plot_enrichment: Plot module from bio_enrich

View source: R/biological_integration.R

plot_enrichmentR Documentation

Plot module from bio_enrich

Description

Wrapper of the gprofiler2::gostplot function. Adding support of colorblind palet and selection of subsets if initial multiple query, and/or sources to plot.

Usage

plot_enrichment(
  enrich_output,
  modules = "all",
  sources = "all",
  colorblind = TRUE,
  custom_palette = NULL,
  ...
)

Arguments

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.

Details

Note: The colorblind friendly palette is limited to maximum 8 colors, therefore 8 sources of enrichment.

Value

A plotly object representing enrichment for specified modules

Examples

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)


Kumquatum/GWENA documentation built on July 7, 2023, 3:41 p.m.