rppaList2Heatmap {RPPanalyzer}R Documentation

Draw a heatmap with column side colors from a RPPA data

Description

Draws a heatmap from an RPPA data set and adds column side colors visualizing groups of selected phenodata.

Usage

   rppaList2Heatmap(x, sampledescription = "sample", side.color = "tissue",
   remove = c("blank", "protein", "Abmix"), distance = "euclidean",
   dendros = "both", cutoff = 0.005, fileName = "Heatmap.pdf",
   cols = colorpanel(100, low = "blue", mid = "yellow", high = "red"))

Arguments

x List with RPPA data set, aggregatedreplicates
sampledescription character describing the sample identifier
side.color character describing the parameter for the side colors of the heatmap
remove character describing the arrays that should removed from the heatmap data
distance character describing the method for the dendrogram
dendros character: "both" for row and column dendrogram
cutoff numeric describing the percentage that are identified as outliers for the heatmap color distribution
fileName character for the file where the pdf file will be stored
cols color key for the heatmap

Value

generates a PDF file

Author(s)

Heiko Mannsperger <h.mannsperger@dkfz.de>

Examples

        library(RPPanalyzer)
        data(dataIII)
        dataIII_median <- sample.median(dataIII)
        
        rppaList2Heatmap(dataIII_median)

[Package RPPanalyzer version 1.0.2 Index]