Connect to R

GeMSE uses a connection to R for two applications:

• an alternative way of plotting data (uses R instead of the built-in heatmap function).
• bi-clustering; e.g., see the following figure.

Requirements

• Install R (download and install from any of these mirrors).

• Locate Rscript on your OS. On Microsoft Windows and macOS, it could be in the following paths:

  # Microsoft Windows
  C:\Program Files\R\R-3.4.0\bin\Rscript.exe
  
  # macOS
  /usr/local/bin/Rscript 
  

• make sure the package gplots is installed. To do so, run the following command in R:

  library(gplots)
  

  If you don't receive an error, then the package is installed. You can install this package using the following command:

  install.packages("gplots")
  

• make sure the package ape is installed. You can check it as the following in R:

  library(ape)
  

  If you don't receive an error, then the package is installed. You can install this package using the following command:

  install.packages("ape")
  

Setup GeMSE

On GeMSE main window, go to Tools > Options and choose use R package gplots ( heatmap 2 ) for heatmap. Then write the path to Rscript in the Rscript path textbox. Click on OK button.