plotOldGSEA: Plot using clusterProfiler. 3 GSEA plots are saved to the...

In PNNL-CompBio/amlresistancenetworks: Calculates networks that lead to AML resistance to drugs

Plot using clusterProfiler. 3 GSEA plots are saved to the working directory, two of which are custom to the amlresistancenetworks package.

Description

Plot using clusterProfiler. 3 GSEA plots are saved to the working directory, two of which are custom to the amlresistancenetworks package.

Usage

plotOldGSEA(
  genes.with.values,
  prefix,
  gsea_FDR = 0.05,
  order.by = "NES",
  height = 8.5,
  width = 11,
  ...
)

Arguments

genes.with.values	A data frame with genes as row names, along with a column named "value". Usually this value column consists of log fold changes between two groups.
prefix	string, used for naming the saved plots.
order.by	This determines how the GO terms are sorted. Default is normalized enrichment score "NES", but can also use "p.adjust" to sort by significance of the terms.

PNNL-CompBio/amlresistancenetworks documentation built on Feb. 8, 2025, 11:27 a.m.