plotKEGG: Create a KEGG pathway diagram with DEG data overlay.

In NKInstinct/seqHelpers: Helper Functions for Bulk RNA-Seq Analysis

Create a KEGG pathway diagram with DEG data overlay.

Description

Create a KEGG pathway diagram with DEG data overlay.

Usage

plotKEGG(
  keggData,
  pathway,
  species = "Mouse",
  inputDir = "KEGG Inputs/",
  plotName = NULL,
  geneCols = list(low = "cyan", mid = "white", high = "firebrick"),
  cpdCols = list(low = "blue", mid = "gray", high = "yellow")
)

Arguments

keggData	A dataframe containing MGI symbol-formatted gene IDs,
pathway	A string giving the pathway ID for the pathway of interest, in the format "00001". No species code is required.
species	A string specifying the species to use. Currently, only "Mouse" is supported.
inputDir	A path to a directory where pathview can download the KEGG files. Directory must exist before running this!
plotName	An optional string to append to the output image file. Useful when vectorizing so each subsequent output doesn't overwrite the previous one.
geneCols	A 3-length list giving the low, medium, and high colour values to map to gene expression. Please keep them in that order, names are optional.
cpdCols	As geneCols, but for compound values

Value

Nothing - instead, writes the output png to the working directory. Would love to have it not do that but this seems to be a feature of pathview.

NKInstinct/seqHelpers documentation built on Aug. 20, 2022, 4:30 a.m.