This repository contains the R-scripts for creating heat maps from a cuff links data base. The main script is the heatmaps.R. I suggest sourcing the script.
The script will first ask the user some questions:
- where is the file that contains the list of genes?
- where is the folder with the output of a CuffDiff run?
- where do you want to save the heatmaps?
Next, it will present you with a list of defaults for a bunch of options. It will then ask you if you want to use the defaults. If not, it will prompt you for value for each of the options, one at a time.
Finally, the heatmaps will be created and saved to the output folder.