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]]

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