Question: mouseData in heatmap of metagenomeSeq package
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5.6 years ago by
Guest User12k
Guest User12k 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. metagenomics metagenomeseq • 824 views ADD COMMENTlink modified 5.6 years ago by Joseph Nathaniel Paulson270 • written 5.6 years ago by Guest User12k Answer: mouseData in heatmap of metagenomeSeq package 0 5.6 years ago by United States Joseph Nathaniel Paulson270 wrote: 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="" meta="" genomeseq="" 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. > [[alternative HTML version deleted]]