diagplotDeHeatmap {metaseqR2} | 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

        diagplotDeHeatmap(x, scale = c("asis", "zscore"), con = NULL,
            output = "x11", path = NULL, ...)

### Arguments

`x` | the data matrix to create a heatmap for.
`scale` | value scale in the heatmap. As provided (`scale="asis"`, default) or Z-scores (`scale="zscore"`)
`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 `whichPlot` argument. If `output="x11"`, no output filenames are produced.

### Author(s)

Panagiotis Moulos

### Examples

    dataMatrix <- metaseqR2:::exampleCountData(2000)
    sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
    contrast <- "A_vs_B"
    M <- normalizeEdger(dataMatrix,sampleList)
    p <- statEdger(M,sampleList,contrast)
    diagplotDeHeatmap(dataMatrix[p[[1]]<0.05,])

[Package metaseqR2 version 1.0.11 Index]