I generated a heatmap in R using the following commands:
> mydata <- read.csv(file="Data.csv", header=TRUE, sep=",")
> mydata <- mydata[rowSums(mydata[,-1]^2) >0, ]
> rownames(mydata)=mydata$Name
> mydata <- mydata[,2:253]
> mydatamatrix <- data.matrix(mydata)
> mydatascale <- t(scale(t(mydatamatrix)))
> hr <- hclust(as.dist(1-cor(t(mydatascale), method="pearson")),
method="complete")
> hc <- hclust(as.dist(1-cor(mydatascale, method="spearman")),
method="complete")
> myclhr <- cutree(hr, h=max(hr$height)/2); mycolhr <- sample(rainbow(256));
> myclhc <- cutree(hc, h=max(hc$height)/2); mycolhc <- sample(rainbow(256));
> mycolhr <- mycolhr[as.vector(myclhr)];
> mycolhc <- mycolhc[as.vector(myclhc)];
> library("gplots")
> library("RSvgDevice")
> jpeg("Heatmap.jpg", height=6+2/3, width=6+2/3, units="in", res=1200)
> heatmap.2(mydatamatrix, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc),
dendrogram="both", scale="row", col=brewer.pal(3, "YlOrRd"), cexRow=0.01,
cexCol=0.01,
trace="none", density.info="none", key=TRUE, keysize=1.5,
margin=c(5,8),RowSideColor=mycolhr, ColSideColor=mycolhc)
> dev.off()
I would like to save the file in a graphical format that can be edited later
in any image editing program (like corel). is there a way to do this in R?
Its a lot of data I plotted on heatmap (~ 300*600). The x and y labels are
difficult to read. I used cexRow = 0.01 and cexCol =0.01 with 1200
resolution to save as jpeg file. That helped but I can still hardly figure
out the row labels. I want to be able to read them to interpret the results
and also to edit them with different font/color in corel and may be add
other things that could be relevant to my work. So, I guess my question
here- is there a way I can make the labels readable in R itself or can I
generate a list of the row and col labels (in the exact order as in figure)
in a text file separately so I know the order and can try attaching it to
heatmap in corel draw?
any help will be appreciated! Thanks
BD
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