I am very new to R and don't have any computer program experience whatsoever. I am trying to generate a heatmap of the following data:
Phylum,AI,AJT,BY,GA,Grt,Sm Acidobacteria,0.5,0.7,2.7,0.1,2.6,1.0 Actinobacteria,33.7,65.1,9.7,2.0,3.9,2.1 Bacteroidetes,9.7,5.6,0.7,13.2,41.1,21.6 CCM11b,0.0,0.0,0.0,0.0,0.0,0.1 Chlamydiae,0.1,0.1,0.0,0.0,1.0,0.2 Chlorobi,0.0,0.0,0.0,0.0,0.7,1.0 Chloroflexi,0.1,0.2,0.6,0.2,0.8,0.6 Cyanobacteria,18.7,0.0,1.0,1.5,0.9,0.3 Ellusimicrobiales,0.0,0.0,0.0,0.0,0.0,0.0 Firmicutes,1.0,7.6,8.3,31.9,2.1,6.9 Gemmatimonadetes,5.0,0.3,0.3,0.0,0.1,0.0 GN02,0.0,0.0,0.0,0.0,0.0,0.5 Nitrospirae,0.0,0.2,1.1,0.0,0.0,0.0 NKB19,0.0,0.0,0.9,0.0,0.0,0.0 OP8,0.0,0.1,0.0,0.0,0.0,0.0 OP10,0.6,0.2,0.5,0.0,0.6,0.6 Planctomycetes,0.9,0.5,6.5,2.2,2.0,2.3 Alphaproteobacteria,7.8,10.7,21.8,12.2,5.3,26.8 Betaproteobacteria,9.9,2.8,8.9,21.7,8.3,21.9 Deltaproteobacteria,0.5,0.2,1.8,2.0,1.2,7.1 Epsilonproteobacteria,0.0,0.0,0.0,0.1,0.0,0.2 Gammaproteobacteria,4.0,2.5,8.0,9.4,24.7,5.4 SC4,0.0,0.0,0.0,0.0,0.7,0.0 SM2F11,0.0,0.0,0.0,0.0,0.2,0.0 SPAM,0.0,0.1,0.0,0.0,0.1,0.1 Synergistes,0.0,0.0,0.0,0.1,0.0,0.0 Deinococcus-Thermus,0.0,0.0,0.0,0.0,0.0,0.0 TM6,0.1,0.0,0.0,0.0,0.1,0.0 TM7,0.0,0.1,0.4,0.0,0.4,0.1 Verrucomicrobia,3.8,2.1,23.2,2.9,1.3,0.5 WPS-2,0.0,0.0,0.1,0.0,0.0,0.0 WS3,0.0,0.0,0.0,0.0,0.0,0.1 Uncl Bacteria,3.7,1.2,3.7,0.4,1.9,0.8 I am a microbiologist. What I want to do is construct a heatmap showing the relative abundance of each phylum. The far left column of my table contains all of the phylum names I observed in a set of 6 water samples and each of the columns to the right contains the relative abundance (%) of each phylum in each water sample. I have tried constructing a heatmap using the ggplot guidelines listed at the following site: http://learnr.wordpress.com/2010/01/26/ggplot2-quick-heatmap-plotting/ I can generate a heatmap using this method, but would like to alter the scale. I would like it so that I can have a little more complex gradient ranging from 0% to the highest relative abundance that I observe in the above table (65.1%). The default scale I get using the link above is just a relative intensity scale ranging from 1 to 5 (where white represent low percentages and steelblue represented high percentages). This is alright but for phyla that are present at relative abundance of less than 5% all appear to be white (or non-existant). Is there anyway to fix this? Any help would be greatly appreciated. Thanks, Chris ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.