heatplot() 1. red-*black*-green palette, 2.suppress drawing of the row dendrogram (but NOT row reordering)
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Amos Folarin ▴ 80
@amos-folarin-4200
Last seen 9.9 years ago
Hi Karl, You can plot your palet based on whatever colorscheme you want i.e. redgreen() or greenred(). If you want black omitted then maybe try building a custom colorpanel(n, low, mid, high), where you specify your own mid point color. I see you already have some ordering set for your Rows and Cols. Error in heatmap.2(data, Colv = Colv, Rowv = Rowv, col = plotcols, scale = scale, : the dendrogram plotting is controled by the dendrogram arg. dendrogram = c("both","row","column","none"), I'm not sure why this is not matching the arguement correctly (suggest you post the actual code you are using). but dendrogram="column" should work. There is a good tutorial here -- see end of: http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/r/heatmap/ Regards, Amos Folarin [[alternative HTML version deleted]]
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k. brand ▴ 420
@k-brand-1874
Last seen 9.9 years ago
Hi Amos, Thank you for your comments & suggestions. Unfortunately i still haven't found a simple way to get black *INTO* my heatplot() palette (not remove as was mis-communicated in my previous email). #This is the actual code i attempted to get black into the palette #Attempt red/black/green palette with heatmap.2() "col=" argument: library(made4) my.mat <- matrix(rnorm(250), nrow=50, ncol=5) windows() plot.new() heatplot(my.mat, dend="both", cols.default=FALSE, col = c(redgreen(256))) #Using correct heatplot() "lowcol=" argument also fails. #Just get red/green palette: windows() plot.new() heatplot(my.mat, dend="both", cols.default=FALSE, lowcol=c(colorpanel(256, low="green", mid="black", high="red"))) ###end Unless you/some one can demonstrate how, it seems to me heatplot() can only accept a 2 color gradient. So no red-BLACK-green, or any other 3-shade palette with out modifying the heatplot() function. Again any pointers on this appreciated. Re. dendrogram plotting- again, *unlike* heatmap.2, i can not achieve row ordering *without* drawing a row dendrogram. Only choices visible to me- 1. use heatmap.2(), 2. delete post-R eg. with GIMP, or 3. modify heatplot(). Suggestions on this last option also greatly appreciated. With thanks in advance for comments, Karl On 8/7/2010 8:41 PM, Amos Folarin wrote: > Hi Karl, > > You can plot your palet based on whatever colorscheme you want i.e. > redgreen() or greenred(). If you want black omitted then maybe try building > a custom colorpanel(n, low, mid, high), where you specify your own mid point > color. > > I see you already have some ordering set for your Rows and Cols. > Error in heatmap.2(data, Colv = Colv, Rowv = Rowv, col = plotcols, scale = > scale, : > > the dendrogram plotting is controled by the dendrogram arg. dendrogram = > c("both","row","column","none"), I'm not sure why this is not matching the > arguement correctly (suggest you post the actual code you are using). > but dendrogram="column" should work. > > There is a good tutorial here -- see end of: > http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/r/heatmap/ > > > Regards, > Amos Folarin > > [[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 -- Karl Brand Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam T +31 (0)10 704 3457 |F +31 (0)10 704 4743 |M +31 (0)642 777 268
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