Pathway label malposition in GSEA bar plot, and error from duplicated entrez ID from transId mapping

[hzhong-utsw]

Hi,

It's a really nice package. I am using it to run GSEA. But I am facing a few issues. Please kindly help.

1. In my analysis, gene symbol was used. Even though gene symbols are unique, however, when using transId in the genGSEA function, they were mapped to entrez IDs, which could have duplicated values. And the duplicated entrez ID could cause failed in calling GSEA function. It suggests that the mapping from transId has to be one-to-one mapping to make everything work.

2. The second issue is about plotting. See the image attached. The pathway labels in my plot are on the bars, rather than on another side of the bars. It does not happen all the time. Seems random.

Thanks you!
Hua