plot_enrichment: Plot module from bio_enrich

In Kumquatum/GWENA: Pipeline for augmented co-expression analysis

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.