gm_dendplot: gm_dendplot: GSEAmining dendrogram plotter

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 the dendrogram using the dendextend package.

Usage

gm_dendplot(
  df,
  hc,
  col_pos = "red",
  col_neg = "blue",
  dend_len = 30,
  rect = TRUE,
  rect_len = 2
)

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.
col_pos	Color to represent the positively enriched gene sets. Default is red.
col_neg	Color to represent the negatively enriched gene sets. Default is blue.
dend_len	An integer that defines the length of the dendrogram. Default value is 30. The closest to zero the longest the dendrogram.
rect	A logical value indicating if rectangles should be drawn around the clusters to help differentiating them. By default it is set to TRUE.
rect_len	An integer to specify the length of the rectangle around the cluster and the gene set label. Default is 2. The closest to zero the smallest the rectangle.

Value

Invisibly returns a list with all the elements necessary to plot a dendrogram.

Examples

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

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