diagplotDeHeatmap: Diagnostic heatmap of differentially expressed genes

In pmoulos/metaseqR2-local: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

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,])

pmoulos/metaseqR2-local documentation built on May 21, 2024, 3:46 a.m.