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August 29, 2015 14:09
Applying A Divergent Color Scale to A Gene Expression Heat Map
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# Blog Post is here: http://www.nikhilgopal.com/applying-a-divergent-color-scale-to-a-gene-expression-heat-map/ | |
source("http://bioconductor.org/biocLite.R") | |
biocLite("ALL") | |
biocLite("limma") | |
library("ALL") | |
library("limma") | |
data("ALL") | |
eset <- ALL[, ALL$mol.biol %in% c("BCR/ABL", "ALL1/AF4")] | |
heatmap(exprs(eset[1:100,])) | |
f <- factor(as.character(eset$mol.biol)) | |
design <- model.matrix(~f) | |
fit <- eBayes(lmFit(eset,design)) | |
topTable(fit, coef=2) | |
selected <- p.adjust(fit$p.value[, 2]) <0.05 | |
esetSel <- eset [selected, ] | |
heatmap(exprs(esetSel)) | |
heatmap(exprs(esetSel), col=topo.colors(100)) | |
color.map <- function(mol.biol) { if (mol.biol=="ALL1/AF4") "#FF0000" else "#0000FF" } | |
patientcolors <- unlist(lapply(esetSel$mol.bio, color.map)) | |
heatmap(exprs(esetSel), col=topo.colors(100), ColSideColors=patientcolors) | |
library("gplots") | |
heatmap.2(exprs(esetSel), col=topo.colors(10), scale="none", ColSideColors=patientcolors, | |
key=TRUE, symkey=FALSE, density.info="none", trace="none", cexRow=0.5) #generates old heatmap = old10scale.jpg | |
library(RColorBrewer) | |
brewer.pal(n=10, name="RdBu") | |
heatmap(exprs(esetSel), col=brewer.pal(n=10, name="RdBu")) #generates divergent scale heatmap = new.jpg | |
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