rppaList2Heatmap {RPPanalyzer} | R Documentation |
Draws a heatmap from an RPPA data set and adds column side colors visualizing groups of selected phenodata.
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"))
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 |
generates a PDF file
Heiko Mannsperger <h.mannsperger@dkfz.de>
library(RPPanalyzer) data(dataIII) dataIII_median <- sample.median(dataIII) rppaList2Heatmap(dataIII_median)