Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!
Get Started for Free

viewKEGG

viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway

Description

viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway

Usage

viewKEGG(
  obj,
  pathwayID,
  foldChange,
  color.low = "green",
  color.high = "red",
  kegg.native = TRUE,
  out.suffix = "clusterProfiler"
)

Arguments

obj

enrichResult object
pathwayID

pathway ID or index
foldChange

fold change values
color.low

color of low foldChange genes
color.high

color of high foldChange genes
kegg.native

logical
out.suffix

suffix of output file

References

Luo et al. (2013) Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics (Oxford, England), 29:14 1830–1831, 2013. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/content/abstract/29/14/1830.abstract PMID: 23740750

clusterProfiler

statistical analysis and visualization of functional profiles for genes and gene clusters

v3.18.1
Artistic-2.0
Authors
Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Li-Gen Wang [ctb], Giovanni Dall'Olio [ctb] (formula interface of compareCluster)
Initial release

We don't support your browser anymore

Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.