[BioC] mouseData in heatmap of metagenomeSeq package

guest [guest] 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.

> data(mouseData)
> 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(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] 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  
[8] BiocInstaller_1.12.0

loaded via a namespace (and not attached):
[1] 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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