APAVolcano {APAlyzer} | R Documentation

## 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')

[Package APAlyzer version 1.6.0 Index]