Hi there,

By calling *data(mouseData)* you are loading the pre-packaged dataset
included in the metagenomeSeq package.

There are instructions in the vignette on how to import data in Section 2
"Data preparation". It is probably best to call the MRexperiment object
something other than mouseData to ensure your environmental variables
aren't over-written by a load call.

The code to access the
vignette<http://www.bioconductor.org/packages/2.14/bioc/vignettes/metagenomeSeq/inst/doc/metagenomeSeq.pdf>
for
metagenomeSeq is:


vignette("metagenomeSeq")


Hope this helps,

Best wishes.

 - Joseph Paulson


On Mon, Mar 10, 2014 at 3:00 PM, guest [guest] <guest@bioconductor.org>wrote:

>
> 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)
>
> locale:
> [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
> >
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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