Closed mumichae closed 3 years ago
@martaint Is it safe to move all the R/visualization
code here or are you still working on it?
I think it's safe! I'm not working on it :)
On Sat, 6 Mar 2021, 06:05 Michaela Mueller notifications@github.com wrote:
@martaint https://github.com/martaint Is it safe to move all the R/visualization code here or are you still working on it?
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Wow, that's a lot of notebooks! I assume somebody has already checked these are all still relevant?
We removed notebooks some time back (PR), so I think things should be OK. @LuckyMD @danielStrobl Could you double-check if there are any notebooks we don't need anymore?
* Do we need the `.ipynb_checkpoints` directories?
Good point, didn't realise that I was adding those. They should be removed and ignored now.
Should we move the data files in the
visualization/
directory to the topdata/
directory? At least those that are for the paper not just examples for the plotting functions (@martaint might be able to help with that).
I agree, that would be better. If we move the plot data, we just need to update the R scripts accordingly.
Things I think might be removable:
Would love to hear if you think these can be removed or if this is important for reproducibility. If important, then maybe we need a further folder.
The mouse atlas notebooks can be removed I think. I would keep the trajectory_plots and visualisation notebooks as the figures for the supplementary were generated with those. The silhouette graph notebook can be removed.
One thing I noticed is that the notebooks/visualisation.ipynb in master is not the most recent one, it's actually in the recompute_cluster_metrics
branch
Thanks for comments @danielStrobl. Could you say how you would name the folder (or in which existing folder) the notebooks to keep should be put? Just visualization?
Yes, sounds good
One thing I noticed is that the notebooks/visualisation.ipynb in master is not the most recent one, it's actually in the
recompute_cluster_metrics
branch
@danielStrobl Can you open a separate PR for the latest version (or add it here)? Or open an issue I guess, just don't want to forget about this.
P.S. I think you have a pending invite to join this repo, I can resend if you need.
Ok, I'll open a PR for that. That would be great if you could resend the invite.
I agree that the heatmap and mouse atlas notebooks can be removed.
I removed the heatmap plotting script (duplicate) and moved the preprocessing scripts to the Masterinternship_2019 repository.
also, new analysis notebook updates from scIB.
Summarising things that have come up in comments:
Done
.ipynb_checkpoints
directoriesvisualization/img/init
file visualization/atlas_heatmap.ipynb
notebooks/silhouette_graph.ipynb
notebooks/visualization/
Todo
data/
directory (this probably means other changes to scripts so maybe can be a later PR)`notebooks/visualisation.ipynb
to most recent versionAnything that's incorrect or I missed?
Updated 2021-04-22
Also just noticed that each of the dataset notebook folders has an empty README
. We should probably either add some info about the datasets or just delete them. @LuckyMD what do you think?
Could you copy over some text from the dataset description in the paper to the README?
Could you copy over some text from the dataset description in the paper to the README?
That's definitely possible. Alternatively could describe what is in the notebooks (or both).
Or maybe better: everyone could write a small blurb (3-4 sentences of what is in the dataset). I think that could even be from the SI sections.
Check out this pull request on
See visual diffs & provide feedback on Jupyter Notebooks.
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Did some of the minor things, see updated checklist https://github.com/theislab/scib-reproducibility/pull/4#issuecomment-820517623. Main things left to do are double checking notebooks are up to date (@danielStrobl can you help with that?) and deciding what to do with the READMEs.
@lazappi I added a file in scib (https://github.com/theislab/scib/pull/234) which should also be added here in the respective notebook folder. Could you take care of that? Don't want to mess with this PR :) thanks a lot!
Scripts added:
scripts/preprocessing.py
scripts/run_normalize.sh
scripts/sim_norm.py
R/visualization/*
notebooks/*
Corresponding PRs: