Question: Any way to ouput the reordered gene list from heatmap.2()?
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gravatar for Steve Lianoglou
9.7 years ago by
Denali
Steve Lianoglou12k wrote:
Hi Xiang, 1. Please keep replies on list. 2. I've never used the mad4::heatplot function, so I have no idea, sorry. Perhaps someone else can chime in ... I do notice from its help file, though, that it says it internally uses "heatmap" and "dendrogram" functions, so ... -steve On Thu, Jan 21, 2010 at 3:48 PM, xiangxue Guo <xiangxue_guo at="" yahoo.com=""> wrote: > Hi, Steve: > > when use heatplot() in package made4 for a heatmap, Do you know any corresponding function to the " rowInd in heatmap.2()" ? > > Xiang > > --- On Thu, 1/21/10, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > >> From: Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> >> Subject: Re: [BioC] Any way to ouput the reordered gene list from heatmap.2()? >> To: "Juan Lin" <julin at="" aecom.yu.edu=""> >> Cc: bioconductor at stat.math.ethz.ch >> Date: Thursday, January 21, 2010, 10:40 AM >> Hi Juan, >> >> On Thu, Jan 21, 2010 at 12:20 PM, Juan Lin <julin at="" aecom.yu.edu=""> >> wrote: >> > Hi dear all >> > >> > I am using the heatmap.2 function in the gplots >> package to draw a heatmap of >> > 297 gene list. The plot looks very nice. But ?since >> the rows(genes) were >> > reordered along with the dendrogram, is there any way >> to output this >> > reordered gene list from heatmap.2()? >> >> Yes ... take a closer look at the documentation for >> ?heatmap.2 and in >> particular look at the "Value" section. >> >> You'll see that you are (invisibly) returned a list that >> contains a >> component named "rowInd" which contains the permutation of >> rows used >> in the display. So, in your example, simply assign the >> returned value >> from heatmap.2 to a variable, and grab the appropriate >> component, eg: >> >> R> h <- heatmap.2(ht, Rowv=TRUE, ...) >> R> h$rowInd >> >> or >> >> R> rownames(ht)[h$rowInd] >> >> Hope that helps, >> -steve >> >> > >> > >> > >> > The code I used is as below: >> > >> > >> > >> > heatmap.2(ht,Rowv=TRUE,Colv=FALSE, >> > >> > dendrogram= "row", >> > >> > labRow=rownames(ht), >> > >> > distfun = dist, >> > >> > hclustfun = hclust, >> > >> > key=TRUE, >> > >> > keysize=1, >> > >> > lhei=c(0.5,4.5), >> > >> > trace="none", >> > >> > density.info="none", >> > >> > margins=c(3,8), >> > >> > col=rev(redgreen(256)), >> > >> > main="297 genes with high fold change" >> > >> > ) >> > >> > Many thanks! >> > >> > Juan >> > >> > ----------------------------- >> > >> > Juan Lin >> > >> > Faculty Associate >> > >> > Department of Epidemiology and Population Health >> > >> > Albert Einstein College of Medicine >> > >> > >> > >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> ?| Memorial Sloan-Kettering Cancer Center >> ?| Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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