[R] saving heatmaps in graphical format that can be edited in graphic editor tool

[Barry Rowlingson]

On Wed, Sep 8, 2010 at 4:32 PM, BD <bhakti.dwivedi at gmail.com> wrote:
>
> 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!

 I've been doing exactly this today.

 Use the svg() device driver to create an svg file. Then edit it with
"Inkscape", and open-source graphics layout and design program. For a
demo, try:

svg("foo.svg")
plot(1:10)
dev.off()

Then open Inkscape and load foo.svg. You should be able to move all
the bits of the plot around.

 It has saved me a ton of time today, since I wanted to move a legend
on a ggplot graph to make room for another graphic. In Inkscape I can
just select the elements of the legend and drag them around.

 Inkscape is cross-platform, so works on Windows/Mac/Linux I think (am
using the Linux version).

Barry