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  • dacotahm
    Member
    • Oct 2011
    • 28
    #1

    CummeRbund - show individual k-means cluster plots

    I'm using CummeRbund to visualize some RNA-Seq data. I can show expression patterns with this:
    Code:
    ic9 <- csCluster(sigGenes, k=9)
icp9 <- csClusterPlot(ic9)
icp9
    ...but that shows all 9 expression profiles. I would like to show individual plots that have specific patterns. i.e. How do I look at plots 2, 4, 9 individually?
    Tags: cummerbund, ggplot2, rna-seq
    • dacotahm
      Member
      • Oct 2011
      • 28
      #2
      Just to add more detail, the manual section 9.4 (page 39) shows how the clustering is organized. Is there a way to filter and plot only the reads for a specific cluster?

      Bioconductor - Help
      https://bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf
      The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

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