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Question: the order of the column name in heatmap
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gravatar for xiangxue Guo
7.2 years ago by
xiangxue Guo70
xiangxue Guo70 wrote:
HI, Does anybody know how to control the order of the column names displaying in the heatmap (heatplot)? I was trying to compare two heatmaps with same set of genes as row names and same set of patient samples as column names. The result shows a different order of column names. I want they display in the same order in the heatmap pictures. regards, Xiang
ADD COMMENTlink modified 7.2 years ago by Steve Lianoglou12k • written 7.2 years ago by xiangxue Guo70
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gravatar for Steve Lianoglou
7.2 years ago by
Genentech
Steve Lianoglou12k wrote:
Hi, On Thu, Aug 26, 2010 at 2:42 PM, xiangxue Guo <xiangxue_guo at="" yahoo.com=""> wrote: > HI, > > Does anybody know how to control the order of the column names displaying in the heatmap (heatplot)? > > I was trying to compare two heatmaps with same set of genes as row names and same set of patient samples as column names. The result shows a different order of column names. > > I want they display in the same order in the heatmap pictures. You will want to play with the value of the Colv parameter -- try setting it to NULL, or simply an integer vector indicating the order of the columns that you want(?). Read the help for ?heatmap and its explanation for Colv (and Rowv, if you like) to get a better picture, but one of those two should do what you want. -- 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
ADD COMMENTlink written 7.2 years ago by Steve Lianoglou12k
I think, in heatplot, the order is changed because of dengrograms... if they do not require them, try to set them off. Then you will possibly see what you want... Xianghui On Fri, Aug 27, 2010 at 2:58 AM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > On Thu, Aug 26, 2010 at 2:42 PM, xiangxue Guo <xiangxue_guo@yahoo.com> > wrote: > > HI, > > > > Does anybody know how to control the order of the column names displaying > in the heatmap (heatplot)? > > > > I was trying to compare two heatmaps with same set of genes as row names > and same set of patient samples as column names. The result shows a > different order of column names. > > > > I want they display in the same order in the heatmap pictures. > > You will want to play with the value of the Colv parameter -- try > setting it to NULL, or simply an integer vector indicating the order > of the columns that you want(?). > > Read the help for ?heatmap and its explanation for Colv (and Rowv, if > you like) to get a better picture, but one of those two should do what > you want. > > -- > 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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 7.2 years ago by Xianghui Liu10
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