Connect to R - Genometric/GeMSE GitHub Wiki
R
Connect to 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 inR
: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 inR
: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.