Add multiple enrichment methods #49
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| from rpy2.robjects import pandas2ri | ||
| pandas2ri.activate() | ||
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| from ponyo import utils |
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What tensorflow version are you using? If it is less than 2.x.x, your ponyo code might become outdated. (Example Here Really tiny issue in the overall scheme, but I wanted to just let you know.
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Thanks for looking out. I remember having some conflicts with other dependencies that arose when i previously tried to upgrade tensorflow. But it has been a while since I looked at this so I'll make an issue in my ponyo repo, which is using v<2.x.x for tensorflow
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| # Read in config variables | ||
| base_dir = os.path.abspath(os.path.join(os.getcwd(), "../")) |
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Might want to try and use pathlib. I know broken record, but it definitely makes os path generation a lot easier to deal with.
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Not a broken record. I definitely agree with using paths instead of the way I currently have my config. The legacy reason for having the config this way is 1) to be consistent with how ponyo is, which this repo uses and 2) it seemed more user friendly at the time to have a tab-delimited file and have that passed into the notebook as opposed to "importing a python file. I also wasn't aware, at the time when I created the config, that I could define both variables and paths in the same file. But rest assured that my other newer repo uses paths:)
The goal of this PR was to add other multiple enrichment methods to demonstrate the our simulation method can be plugged into other pipelines easily.
The changes to this PR will depend on changes in this PR #50. So for now I want to merge these changes in the in term and I'll open a new PR in the future to finish the work that this PR started.
The main change in this PR can be found in Try_other_enrichment_methods.ipynb. There is not much in this notebook. It mainly starts to outline and setup the changes to be made. This doesn't need a heavy review as this will be changed in the future.