APAVolcano: APAVolcano, APA Volcano plotting

In RJWANGbioinfo/APAlyzer: A toolkit for APA analysis using RNA-seq data

APAVolcano, APA Volcano plotting

Description

APA Volcano plotting

Usage

	APAVolcano (df, Pcol = "pvalue",PAS='3UTR',
						top = -1, markergenes = NULL,
						y_cutoff = 0.05,xlab = "RED", ylab = "-Log10(P-value)",
						PAScolor = c("gray80", "red", "blue"),
						alpha = 0.75, plot_title = NULL,
						width = 4, height = 2.5)	

Arguments

df	a dataframe of APAdiff output
Pcol	p-value column used to for y-axis of volcano plot, default is 'pvalue'
top	number of genes/IPA to label in the plot, default is -1, which don't lable top genes, user can set it >0, e.g., top = 5
markergenes	a set of genes to label in the plot
PAS	type of PAS analyzed, either '3UTR' or 'IPA', default is '3UTR'
y_cutoff	y cutoff line, default is 0.05
xlab	lable of x-axis, default is 'RED'
ylab	lable of y-axis, default is '-Log10(P-value)'
PAScolor	dot color for 'NC','UP' and 'DN' gene/IPAs, default is "gray80", "red", and "blue"
alpha	alpha of the dot, default is 0.75
plot_title	Main title of plot
width	width of the dot, default is 4
height	height of the dot, default is 2.5

Value

The function APAVolcano return a Volcano plot.

Author(s)

Ruijia Wang

Examples

    library("TBX20BamSubset")
    library("Rsamtools")
    flsall = getBamFileList()
    extpath = system.file("extdata",
    "mm9_TBX20.APAout.RData", package="APAlyzer")
    load(extpath)
    sampleTable1 = data.frame(samplename = c(names(flsall)),
        condition = c(rep("NT",3),rep("KD",3)))
    sampleTable2 = data.frame(samplename = c("SRR316184","SRR316187"),
        condition = c("NT","KD"))
    ## 3'UTR APA plot
    test_3UTRmuti=APAdiff(sampleTable1,DFUTRraw,
    conKET='NT',trtKEY='KD',PAS='3UTR',CUTreads=0)
	UTR_APA_PLOT=APAVolcano(test_3UTRmuti, PAS='3UTR', Pcol = "pvalue", top=5, plot_title='3UTR APA')

    ## IPA plot
    test_IPAmuti=APAdiff(sampleTable1,IPA_OUTraw,
    conKET='NT',trtKEY='KD',PAS='IPA',CUTreads=0)
	IPA_PLOT=APAVolcano(test_IPAmuti, PAS='IPA', Pcol = "pvalue", top=5, plot_title='IPA')

RJWANGbioinfo/APAlyzer documentation built on Dec. 6, 2024, 3:36 p.m.