[R] color palette for heatmap?
Hi, Does anyone know how I can specify the colors based on the data values in heatmap? I have values ranging from -4 to 25 and I want to specify colors as: -4 = white 0 = white/snow 10 =darkblue 20 = red 25 = dark red the command line that I am currently using is (which is close to what I want but not exactly) col=colorRampPalette(c(-5 = white,5 = white, 10 = darkblue, 20 = red))(4) can I get a smooth transition in heatmap colors from white to blue to red in R? Thanks! -- View this message in context: http://r.789695.n4.nabble.com/color-palette-for-heatmap-tp3219238p3219238.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] How to Ignore NaN values in Rows when using hclust function in making Heatmap??
I am making heatmaps for a dataset (~ 300*600 matrix) with the following R script (I am not familiar with R and this is the first time I am using it). library(gplots) library(Cairo) mydata - read.csv(file=data.csv, header=TRUE, sep=,) rownames(mydata)=mydata$Name mydata - mydata[,2:297] mydatamatrix - data.matrix(mydata) mydatascale - t(scale(t(mydatamatrix))) hr - hclust(as.dist(1-cor(t(mydatascale), method=pearson)), method=complete) hc - hclust(as.dist(1-cor(mydatascale, method=spearman)), method=complete) myclhr - cutree(hr, h=max(hr$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)]; jpeg(scaleRow.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=rev(heat.colors(10)), cexRow=0.08, cexCol=0.08, trace=none, density.info=none, symkey= FALSE, key=TRUE, keysize=1.5, margin=c(5,8),RowSideColor=mycolhr, ColSideColor=mycolhc) dev.off() My question is, in the dataset I have good number of rows (~ 17) that has zero value for all the columns defined. So when I run these two command lines, hr - hclust(as.dist(1-cor(t(mydatascale), method=pearson)), method=complete) hc - hclust(as.dist(1-cor(mydatascale, method=spearman)), method=complete) I get the error msg: error in hclust (as.dist(1-cor(t(mydatascale), method=pearson)), : NA/NaN/Inf in foreign function call (arg 11). It seems to be a problem when NaN exist in all columns for a given row. Because, when I delete those rows the script runs fine. I don't know how to work my way around this error msg. I have to include these rows and also cluster them in the heatmap. Is there a way to do this? Please help me! In addition to above, in my dataset I have duplicate row names. I want to keep it that way but every time I run a script I get a warning message for not having unique row names. Is there a way I can ignore this message and still keep my original row names instead of re-naming them? Thanks!! -- View this message in context: http://r.789695.n4.nabble.com/How-to-Ignore-NaN-values-in-Rows-when-using-hclust-function-in-making-Heatmap-tp2551032p2551032.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] How to include rows with zeros in all columns when clustering data for heatmap?
I am making a heatmap. In the dataset, I have couple of rows with zero value in all the columns. When I cluster data using hierarchical clustering, R gives an error message. When I get rid of those particular rows, the script runs smoothly with no problem. I have to include those rows somehow and also need to cluster the data. Is there a way around to do this? BD -- View this message in context: http://r.789695.n4.nabble.com/How-to-include-rows-with-zeros-in-all-columns-when-clustering-data-for-heatmap-tp2544115p2544115.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] saving heatmaps in graphical format that can be edited in graphic editor tool
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 -- View this message in context: http://r.789695.n4.nabble.com/saving-heatmaps-in-graphical-format-that-can-be-edited-in-graphic-editor-tool-tp2531512p2531512.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] saving heatmaps in graphical format that can be edited in graphic editor tool
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.comml-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=nodenode=2531559i=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=nodenode=2531559i=1mailing 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 herehttp://r.789695.n4.nabble.com/template/TplServlet.jtp?tpl=unsubscribe_by_codenode=2531512code=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.
