diagplot.de.heatmap {metaseqR} | R Documentation

## Diagnostic heatmap of differentially expressed genes

### Description

This function plots a heatmap of the differentially expressed genes produced by the metaseqr workflow, useful for quality control, e.g. whether samples belonging to the same group cluster together.

### Usage

        diagplot.de.heatmap(x, con = NULL, output = "x11",
            path = NULL, ...)

### Arguments

`x` | the data matrix to create a heatmap for.
`con` | an optional string depicting a name (e.g. the contrast name) to appear in the title of the volcano plot.
`output` | one or more R plotting device to direct the plot result to. Supported mechanisms: `"x11"` (default), `"png"`, `"jpg"`, `"bmp"`, `"pdf"`, `"ps"`.
`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)
    diagplot.de.heatmap(data.matrix[p[[1]]<0.05,])

[Package metaseqR version 1.28.0 Index]