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Question: qustion on heatmap
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gravatar for sidahmed BENABDERRAHMANE
7.4 years ago by
Hello I have a similarity matrix between a set of genes with which I want to generate a heatmap, for this reason let me ask some questions: - Is it possible to change the color of a cell of the heatmap after its creation? because I want to keep the upper triangle of the heatmap to display the color assigned to the similarity measure between genes, and in the lower triangle of the heatmap I want to use its cells to display other information. thank you in advance ------ B.S. (benabdsi at loria.fr) INRIA France.
ADD COMMENTlink modified 7.4 years ago by James W. MacDonald45k • written 7.4 years ago by sidahmed BENABDERRAHMANE30
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gravatar for James W. MacDonald
7.4 years ago by
United States
James W. MacDonald45k wrote:
Hi B.S., On 7/20/2010 6:18 AM, sidahmed BENABDERRAHMANE wrote: > Hello > > I have a similarity matrix between a set of genes with which I want to > generate a heatmap, for this reason let me ask some questions: > > - Is it possible to change the color of a cell of the heatmap after its > creation? because I want to keep the upper triangle of the heatmap to > display the color assigned to the similarity measure between genes, and > in the lower triangle of the heatmap I want to use its cells to display > other information. When you use the term 'heatmap', the connotation is that you want to do some sort of clustering rather than a simple similarity matrix, and that is what the various heatmap functions in R are designed to do. So, no it isn't possible to use any of the heatmap functions to do what you want. That said, the heatmap functions are all pretty much just wrappers around the image() function, and as R is a scripting language it wouldn't be that difficult to write a function to do what you want. Just make a matrix of the data you want to create an image of, and then plot. The image() function is a bit tricky as to the orientation of the resulting image, so you should look at the help file. The code for the heatmap() function might also be useful. Best, Jim > > thank you in advance > > ------ > B.S. (benabdsi at loria.fr) > INRIA France. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENTlink written 7.4 years ago by James W. MacDonald45k
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