diagplot.volcano {metaseqR} | R Documentation

## (Interactive) volcano plots of differentially expressed genes

### Description

This function plots a volcano plot or returns a JSON string which is used to render aninteractive in case of HTML reporting.

### Usage

        diagplot.volcano(f, p, con = NULL, fcut = 1, pcut = 0.05,
            alt.names = NULL, output = "x11", path = NULL, ...)

### Arguments

`f` | the fold changes which are to be plotted on the x-axis.
`p` | the p-values whose -log10 transformation is going to be plotted on the y-axis.
`con` | an optional string depicting a name (e.g. the contrast name) to appear in the title of the volcano diagplot.
`fcut` | a fold change cutoff so as to draw two vertical lines indicating the cutoff threshold for biological significance.
`pcut` | a p-value cutoff so as to draw a horizontal line indicating the cutoff threshold for statistical significance.
`alt.names` | an optional vector of names, e.g. HUGO gene symbols, alternative or complementary to the unique names of `f` or `p` (one of them must be named!). It is used only in JSON output.
`output` | one or more R plotting device to direct the plot result to. Supported mechanisms: `"x11"` (default), `"png"`, `"jpg"`, `"bmp"`, `"pdf"`, `"ps"` or `"json"`. The latter is currently available for the creation of interactive volcano plots only when reporting the output, through the highcharts javascript library.
`path` | the path to create output files.
`...` | further arguments to be passed to plot devices, such as parameter from `par`.

### Value

The filenames of the plots produced in a named list with names the `which.plot` argument. If `output="x11"`, no output filenames are produced.

### Author(s)

Panagiotis Moulos

### Examples

    require(DESeq)
    data.matrix <- counts(makeExampleCountDataSet())
    sample.list <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
    contrast <- "A_vs_B"
    M <- normalize.edger(data.matrix,sample.list)
    p <- stat.edger(M,sample.list,contrast)
    ma <- apply(M[,sample.list$A],1,mean)
    mb <- apply(M[,sample.list$B],1,mean)
    f <- log2(ifelse(mb==0,1,mb)/ifelse(ma==0,1,ma))
    diagplot.volcano(f,p[[1]],con=contrast)
    #j <- diagplot.volcano(f,p[[1]],con=contrast,output="json")

[Package metaseqR version 1.28.0 Index]