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greenelab / ADAGEpath

An R package (ADAGEpath) to perform signature analysis using methodology from the ADAGE manuscript
BSD 3-Clause "New" or "Revised" License
6 stars 6 forks source link

Activity heatmap and signature annotation #4

Closed tj8901nm closed 8 years ago

tj8901nm commented 8 years ago

This PR has two main files to review: annotate_signature.R and cal_activity.R. annotate_signature.R: newly added, contains functions to associate ADAGE signatures to GO/KEGG terms. cal_activity.R: add a new function plot_activity_heatmap.R.

Sorry, I forgot to push back after merge again... Other than this, should be quite straightforward.

gwaybio commented 8 years ago

Old commits are still showing up! This makes a pull request review more difficult since it is often nice to review commit by commit if there are descriptive commit messages and a more complicated/longer changeset. I have had this issue before so I know what is going on!

Essentially, your commits are getting merged into greenelab/ADAGEpath master (upstream/master) but not getting merged back into tj8901nm/ADAGEpath master. To alleviate this, here is what I do after merging a pull request:

git checkout master
git fetch upstream
git merge upstream/master
git push

When I was making this error before, I was forgetting the push at the end!

tj8901nm commented 8 years ago

Thanks @gwaygenomics. I think I also omitted the git push step. Will keep in mind next time!