broadinstitute/dropviz

Incorporate curation_sheet for CB 7

Closed this issue · 2 comments

Cerebellum Cluster 7 currently is missing from the DropViz app data.
This is because the cluster_sheet was accidentally not included. Arpy created a replacement at /Volumes/broad_mccarroll/dropseq/data/clusters/atlas_ica/arpy_test/F_GRCm38.81.P60Cerebellum_ALT/cluster_sheets/Cluster_7.csv, but rerunning prep will cause bookmarking to break.

See email from Arpy on Apr 9, 2018 "discovered a missing "cluster_sheet" in the Cerebellum dataset, wanted to let you know".

The main problem that I can think of right now is that I assign a "c.id" unique cluster ID to each cluster and this number is used in the UI, so is part of the state in the bookmark. Those c.id values are simple integers assigned on-the-fly at startup based on the order of all the rows in cluster.names_.
See

) %>% mutate(c.id=1:length(exp.label))

Same issue with sc.id for subclusters.

Maybe the right workaround is to ensure that the newly generated cluster.names_ and subcluster.names_ retain all the same order except that cluster 7 is appended. Maybe that means hard-coded an arrange in prep-global.R.

Instead of hard-coding an old order in prep-global.R, I think the right thing to do is to regenerate the data and manually replace the few bookmarks in the manuscript that reference cluster comparison.
I can go through all of the bookmarks in the current manuscript and make a note of those that will need replacing.