[BioC] mouseData in heatmap of metagenomeSeq package
guest at bioconductor.org
Mon Mar 10 20:00:00 CET 2014
Dear Bioconductor users,
I would like to plot heatmap with metagenomics dataset, I have 48 mouse samples that were distributed into 8 groups. I copied my dataset as the same format to metagenomeSeq directory for importing the dataset. Everything seems fine till I tried to plot heatmap. I copied the scripts from the tutorial.
> trials = pData(mouseData)$diet
> heatmapColColors = brewer.pal(12, "Set3")[as.integer(factor(trials))]
> heatmapCols = colorRampPalette(brewer.pal(9, "RdBu"))(50)
> # plotMRheatmap
> plotMRheatmap(obj = mouseData, n = 200, cexRow = 0.4, cexCol = 0.4, trace = "none", col = heatmapCols, ColSideColors = heatmapColColors)
When I looked at the heatmap, it is not my dataset, it is still from the example dataset. When I checked on the scripts again, I didn't see any script to help build mouseData with the new dataset. COuld you instruct how I load my dataset into mouseData? or any other solutions?
Thanks a lot, I do appreciate it.
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
attached base packages:
 parallel stats graphics grDevices utils datasets methods base
other attached packages:
 metagenomeSeq_1.4.0 gplots_2.12.1 RColorBrewer_1.0-5 matrixStats_0.8.14 limma_3.18.13 Biobase_2.22.0 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
 bitops_1.0-6 caTools_1.16 gdata_2.13.2 gtools_3.3.1 KernSmooth_2.23-10 R.methodsS3_1.6.1 tools_3.0.2
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