Frustrated by the poor quality of the output of the desktop version javaGSEA (i.e., low resolution, only in pixel-based format, etc), I have written the function
replotGSEA to re-plot data from the javaGSEA desktop version. The function takes three arguments:
path, the path to the javaGSEA output folder;
gene.set, which is the name of the gene set you want to plot (note: approximate matching is used in a grep-function to determine the appropriate gene set); and
class.name, which is the name of the variable to which gene expression has been matched (i.e., the description of the variable that is specified in the .cls file or that is used to pre-rank the data; example: "drug treatment"). An example of the output is below. Please note that R can generate pdfs, allowing for vector-based output (unfortunately I cannot link pdfs in this post and have to use .png format instead). I have posted the code on GitHub. Comments on the output are welcome! I hope you find this useful.
* EDIT: I have now updated the tool and included the possibility to use custom metric ranges other than [-1, 1] *
* EDIT2: Upon feature request, I have now updated the tool and included the possibility to use custom enrichment score ranges *