plotGSEA: Function "plotGSEA"

In Coraline66/RNASeqAnalysis: Perform RNASeq Data Analysis

Description

This function generates variety of plots from GSEA result

Usage

plotGSEA(data_info, gseaRes, gs, gs_name, geneRank, gene.esI, title, K,
  type, attr1, attr2, conditionI, conditionII, N, H1, W1, H2, W2, H3, W3)

Arguments

data_info	data frame containing clinical information
gseaRes	the result from GSEA
gs	geneset "CORALINE Signature" generated from our cohort
gs_name	the geneset used for GSEA based on gene names
geneRank	the gene ranking used for GSEA
gene.esI	expression set of normalized gene counts matrix based on gene names
title	a string character indicating the name of geneset
K	number of top enriched/significant pathways to be plotted
type	a character indicating the group condition
attr1	a character indicating the column name of sample IDs in the clinical data
attr2	a character indicating the column name of desired group in the clinical data
conditionI	a character vector indicating the primary group condition
conditionII	a character vector indicating the secondary group condition
N	a variable indicating one of the value from attr2
H1	height for plotting significant pathways
W1	width for plotting significant pathway
H2	height for plotting enriched pathways
W2	width for plotting enriched pathways
H3	height for ES plot
W3	width for ES plot

Value

a list of plot object

Coraline66/RNASeqAnalysis documentation built on Nov. 25, 2019, 8:03 a.m.