
Thanks!  I will try it now.  I am using linux too!

Bhakti

On Wed, Sep 8, 2010 at 11:54 AM, Barry Rowlingson [via R] <
ml-node+2531559-939380251-160152@n4.nabble.com<ml-node%2B2531559-939380251-160152@n4.nabble.com>
> wrote:

> On Wed, Sep 8, 2010 at 4:32 PM, BD <[hidden email]<http://user/SendEmail.jtp?type=node&node=2531559&i=0>>
> 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
>
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