cluster and plot (gene expression) data

  1. Open RStudio or an R terminal.
  2. Assuming your files are stored in bi/fancy-project/, set the correct working directory:
  3. Read the data and convert to a matrix Note that a txt file is read (column separator is tab). You can export a tab-delimited text file from your favorite spreadsheet software. If you choose to export to a CSV, make sure you change the sep="\t" param to sep=",". See here.
  4. Cluster column and row data
  5. Create a heatmap and plot to a PDF file

Install cummeRbund on Ubuntu 14.04/ Linux Mint 17.3

Update R to the latest version.

Ubuntu 14.04/ Linux Mint 17.3: Update R

Get the latest pre-build deb file here: cran.es.r-project.org

access a subset of rows/ columns

sort/ order data table by comlumn

access first row/ column in a data table

First row: Row by identifier: First column: