plotPCA_pickPCs: Plot principal components analysis: DESeq2 method, but more...

In kmuench/DESeqAid: DESeqAid: Kristin's favorite functions for her DESeq-based differential expression pipelines

Description

This function allows you to plot a Principal Components Analysis with more than the first two PCs. It uses the same method implemented by DESeq (and is, in fact, an edited version of the plotPC function). Code courtesy Santosh Anand: https://www.biostars.org/p/243695/

Usage

plotPCA_pickPCs(object, intgroup = "condition", PC_A, PC_B, num_A, num_B,
  ntop = 500, returnData = FALSE)

Arguments

object	DESeq object, e.g. DESeqTransform
intgroup	Character string describing how you want to color the points
PC_A	Character string with name of first PC to plot, e.g. 'PC2'
PC_B	Character string with name of second PC to plot, e.g. 'PC3'
num_A	Integer corresponding to number of PC_A to plot
num_B	Integer corresponding to number of PC_B to plot
ntop	Number of genes to use when calculating PCs
returnData	Return PC data for plotting, or just use this plot?

Details

At some point, this code will be rewritten so you don't have to define your PCs of interest twice.

Examples

plotPCA_pickPCs(dds_kal_vst_bc, 'PCR_integration', 'PC2', 'PC3', 2, 3, returnData=TRUE)

kmuench/DESeqAid documentation built on Oct. 14, 2020, 4:45 a.m.