plot_fgsea: Plot fGSEA output

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Plot fGSEA output

Description

Plot heatmap with enrichment scores by contrast

Usage

plot_fgsea(
  x,
  trim = 70,
  sets,
  nes = TRUE,
  cluster_row = FALSE,
  cluster_col = FALSE,
  ...
)

Arguments

x	list from link{fgsea_all}
trim	trim long names, default more than 70 characters
sets	display contrasts sharing n or more sets for n > 1. If n = 1, then only plot unique sets. If missing, then plots all sets, default.
nes	plot NES (or ES if FALSE)
cluster_row	Cluster dendrogram rows, default is an alphabetical list
cluster_col	Cluster dendrogram columns, default FALSE
...	other options passed to pheatmap

Author(s)

Chris Stubben

Examples

## Not run: 
  library(hciRdata)
  fc <- write_gsea_rnk(res, write=FALSE)
  x <- fgsea_all(fc, msig_pathways$KEGG, FDR= 0.25)
  plot_fgsea(x)
 
## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on Aug. 20, 2024, 12:22 a.m.