Message-ID: <1336551261670-4619683.post@n4.nabble.com>
Date: 2012-05-09T08:14:21Z
From: BrittD
Subject: Matrix heatmap
In-Reply-To: <1336522672422-4619084.post@n4.nabble.com>
I would leave my table as a heatmap where darker colors represent higher
similarity, and the lighter colors represent less level of similarity.
I'm using version 2.11 of R.
I once used this code, maybe it will help you:
#dendogram
plot(dendro15, labels = cellType) ### I first made a dendrogram of my data
#heatmap specifications
# Filter genes on variance otherwise the heatmap cannot be shown.
em <- exprs(ALL)[which(apply(exprs(ALL), 1, sd) > 1.75), ] #### I had so
many genes I had to filter them
pal <- maPalette(low="blue", high="yellow", mid=NULL, k=25) #### You can
make a color palet here to specify
## the light and dark colors.
### Heatmap
heatmap(em, Colv=as.dendrogram(dendro15), col=pal, labCol=cellType)
--
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