plotVolcanoII: Function "plotVolcanoII"

In Coraline66/RNASeqAnalysis: Perform RNASeq Data Analysis

Description

This function generates volcano plot

Usage

plotVolcanoII(palette = c("red2", "royalblue", "grey70"), fc = 0.2,
  pval = 0.1, linetype = "solid", res, attr1, attr2,
  showLegend = TRUE, mytitle, group, UPgenes, DWgenes, xmin, xmax, ymin,
  ymax, W, Date)

Arguments

palette	a vector of colors used in plotting the volcano. Default is c("red2", "royalblue", "grey70").
fc	a numeric variable representing the log2FoldChange cutoff. Default is 0.2
pval	a numeric variable representing the adjusted p value cutoff. Default is 0.1
linetype	a character variable indicating the line type for hline and vline. Default is 'solid'.
res	a data frame containing the differential gene expression analysis result(log2FoldChange and padj)
attr1	a character indicating column name of log2FoldChange
attr2	a character indicating column name of adjusted p value
showLegend	logical, indicating whether to show the legend. Default is TRUE.
mytitle	a string character indicating the title of the plot
group	a string character indicating the group condition
UPgenes	"up-regulated" pathway in the given geneset
DWgenes	"down-regulated" pathway in the given geneset
xmin	the minimum of x axis
xmax	the maximum of x axis
ymin	the minimum of y axis
ymax	the maximum of y axis
W	a numeric variable indicating the width of the plot
Date	a Date object obtained from Sys.Date

Value

a list consisting of normalized gene expression matrix.

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