RPPanalyzer (version 1.3)

rppaList2Heatmap: 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 = "eucsq",
   dendros = "both", cutoff = 0.005, fileName = NULL,
   cols = colorpanel(100, low = "blue", mid = "yellow", high = "red"),
   hclust.method="ward", scale = "row")

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. If NULL, plot to standard plotting device.

cols

color key for the heatmap

hclust.method

The method to be used for cluster agglomeration. Defaults to ward. See help of hclust for options.

scale

String. Either row, column, both or none for row or column, both or no scaling, respectively.

Value

• generates a PDF file

Examples

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