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+2531559-939380251-160...@n4.nabble.com<ml-node%2b2531559-939380251-160...@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 > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=2531559&i=1>mailing > list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > > ------------------------------ > View message @ > http://r.789695.n4.nabble.com/saving-heatmaps-in-graphical-format-that-can-be-edited-in-graphic-editor-tool-tp2531512p2531559.html > To unsubscribe from saving heatmaps in graphical format that can be edited > in graphic editor tool, click > here<http://r.789695.n4.nabble.com/template/TplServlet.jtp?tpl=unsubscribe_by_code&node=2531512&code=Ymhha3RpLmR3aXZlZGlAZ21haWwuY29tfDI1MzE1MTJ8LTE3NjEyNTUyNg==>. > > > -- View this message in context: http://r.789695.n4.nabble.com/saving-heatmaps-in-graphical-format-that-can-be-edited-in-graphic-editor-tool-tp2531512p2531575.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
