Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • 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.

        Comment

        Previous template Next

        Latest Articles

        Collapse
        • SEQadmin2
          16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
          by SEQadmin2




          NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
          Today, 06:46 AM
        • SEQadmin2
          Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
          by SEQadmin2



          Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

          Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating          ...
          10-14-2026, 09:55 AM
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        Genome Sequencing Reveals Large, Repeat-Rich DNA in Trapdoor Spider Named for Stephen Colbert by SEQadmin2
        Started by SEQadmin2, 10-28-2026, 09:57 AM
        0 responses
        22 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-28-2026, 09:57 AM  
        Single-Cell Sequencing of 5 Million Immune Cells Links Genetic Variants to Disease by SEQadmin2
        Started by SEQadmin2, 10-28-2026, 09:51 AM
        0 responses
        14 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-28-2026, 09:51 AM  
        Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 11:13 AM
        0 responses
        68 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 11:13 AM  
        Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 10:48 AM
        0 responses
        48 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 10:48 AM  
        View All
        Working...