rppaList2Heatmap: Draw a heatmap with column side colors from a RPPA data

In RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array 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

Author(s)

Heiko Mannsperger <[e-mail]>

Examples

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

Example output

The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
[1] "Discarding 37values below lower 0.5% quantile and 37 values above upper 99.5% quantile"

RPPanalyzer documentation built on May 2, 2019, 6:10 p.m.