gm_enrichterms: gm_enrichterms: GSEAmining enriched terms

In GSEAmining: Make Biological Sense of Gene Set Enrichment Analysis Outputs

Description

Takes the output of gm_clust, which is an hclust class object, and plots gene set enriched terms as wordclouds. Two options are available, either separate enrichments by clusters or plot them together in a single plot.

Usage

gm_enrichterms(df, hc, clust = TRUE, col_pos = "red", col_neg = "blue")

Arguments

df	Data frame that contains at least three columns: an ID column for the gene set names, a NES column with the normalized enrichment score and a core_enrichment column containing the genes in the leading edge of each gene set separated by '/'.
hc	The output of gm_clust, which is an hclust class object.
clust	A logical value indicating if wordclouds should be separated by clusters or not. Default value is TRUE.
col_pos	Color to represent positively enriched gene sets. Default is red.
col_neg	Color to represent negatively enriched gene sets. Default is blue.

Value

Returns a ggplot object.

Examples

data(genesets_sel)
gs.cl <- gm_clust(genesets_sel)
gm_enrichterms(genesets_sel, gs.cl)

GSEAmining documentation built on Nov. 8, 2020, 5:52 p.m.