plotGeneScore: Plot gene (DE/DS) scores

In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description

This function is to plot gene scores, as well as DE scores and DS scores

Usage

plotGeneScore(score, perm.score = NULL, pdf = NULL, 
              main = c("Overall", "Expression", "Splicing"))

Arguments

score	the gene/DE/DS score vector.
perm.score	a matrix of the corresponding gene/DE/DS scores on the permutation data sets.
pdf	if a PDF file name provided, plot will be save to that file.
main	the key words representing the type of scores that will be shown in the plot main title.

Details

The plot shows the ranked scores from the largest to the smallest. Lines also show the maximum and average scores, values shown on the top left.

Author(s)

Xi Wang, [e-mail]

Examples

data(DEscore, package="SeqGSEA")
plotGeneScore(DEscore, main="Expression")
data(DSscore, package="SeqGSEA")
gene.score <- geneScore(DEscore, DSscore, method="linear", DEweight = 0.3)
plotGeneScore(gene.score)

sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.