Hi all, I am working on a gene expression analysis. I want to plot the heatmap resulting from the clustering (for both arrays and genes) I am generating this plot with image() function with a red-black-green color palette but the resulting image has a really poor contrast (because of the extreme expression values most of the image is dark) Is there a known graphical parameter or a simple idea which I can use to obtain an image with good contrast ? (As we usually do in the pixels settings with treeview software ) Best, Tony ps : I don't wanna use existing packages like heatmap or heatmap.plus as I am customizing distances and linkage. thanks ! [[alternative HTML version deleted]]

On Tue, Apr 13, 2010 at 8:52 AM, Anthony Ferrari <ferraria at="" gmail.com=""> wrote: > Hi all, > > I am working on a gene expression analysis. > I want to plot the heatmap resulting from the clustering (for both arrays > and genes) > > I am generating this plot with image() function with a red-black- green color > palette but the resulting image has a really poor contrast (because of the > extreme expression values most of the image is dark) > > Is there a known graphical parameter or a simple idea which I can use to > obtain an image with good contrast ? (As we usually do in the pixels > settings with treeview software ) Have a look at the breaks argument. > ps : I don't wanna use existing packages like heatmap or heatmap.plus as I > am customizing distances and linkage. You can also customize these properties in heatmap, heatmap.2, etc. See the help. Sean

Hi Tony One way of improving contrast (but loosing the quantitative scale) is to rank-transform the image. By definition, this uses the available color range uniformly. Example: library(affydata) data("Dilution") image(Dilution[,1], transfo=function(x) x) image(Dilution[,1], transfo=rank) ## the default for 'transfo' here is 'log') Best wishes Wolfgang Anthony Ferrari ha scritto: > Hi all, > > I am working on a gene expression analysis. > I want to plot the heatmap resulting from the clustering (for both arrays > and genes) > > I am generating this plot with image() function with a red-black- green color > palette but the resulting image has a really poor contrast (because of the > extreme expression values most of the image is dark) > > Is there a known graphical parameter or a simple idea which I can use to > obtain an image with good contrast ? (As we usually do in the pixels > settings with treeview software ) > > Best, > > Tony > > ps : I don't wanna use existing packages like heatmap or heatmap.plus as I > am customizing distances and linkage. > > thanks ! > > [[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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber