trvrb
commented
9 months ago Adding to this... I was just wanting to recomposite manuscript Figure 2C (the exploded tree) and found https://github.com/blab/ncov-king-county/blob/main/analysis/figures/mcc_tree_plotting.ipynb to do so. However, a couple flags here:
- These notebooks should be renamed to match final figure labels
- The use of absolute path
bt.loadNexus('/Users/mparedes/Desktop/new_variants_pull/mcc_tree_random_3000.trees')prevents me (and others) from being able to run this notebook. Please version the MCC tree and refer to it here as a relative path.
miparedes
[x]
git rm -f .ipynb_checkpointswherever they occur and add.ipynb_checkpointsto.gitignore.[x] Also force remove and add
.Rhistoryand.RDatato.gitgnore[x] Add
README.mdfiles that give context to top-level directoriesanalysisandmascot_glm. There is not nearly enough instructions here for someone to be able to reproduce the results. You want the readme to make it clear to run command X, followed by command Y, etc.... Here's an example: https://github.com/blab/dengue-antigenic-dynamics/tree/master/titer_model. It looks like the top-level readme has a start on this, but I don't think it's detailed enough.For instance,
[x] You're missing important intermediate files. Just as an example, if I try to run the notebook above
mascot_glm/data_for_tsv) /combining_metadata_and_cluster_assignments.ipynb, it referencesnewickpath = "../../nextstrain_build/results/other_tree.nwk", but there is noresults/directory here.[x] You should be versioning results (especially the
.mcctree and the.logfile) from themascot_glm/analysis. I don't see this here. Also version the MASCOT GLM XML, but exclude sequences given GISAID requirements.[x] Move
figures/to top-level directory and make each figure its own clean.ipynb(unless grouping really makes sense). Take a look at https://github.com/blab/adaptive-evolution/tree/master/adaptive-evolution-analysis for a good example of this.