Append cell meta cluster labels to cell table #567
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
…t appending of meta cluster labels
|
Sorry I already approved the changes, but I just thought of a possible use case that might cause an error with this implementation. For very small cells (or weird cells), it's possible they're not included in the cell clustering (if there are no pixel clusters in there). In that case, the cell table and the cell clustering output wouldn't have the same entries. It would probably best to have those say "Unassigned" or something like that in the metacluster column in the cell table. |
ngreenwald
requested changes
May 27, 2022
ngreenwald
approved these changes
May 28, 2022
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
What is the purpose of this PR?
Closes #551 and closes #523. The cell table is a requirement for several downstream analysis scripts, not just pixel clustering. To ensure analysis can be performed based on the cell meta cluster labels, these will need to be appended to the cell table as well.
How did you implement your changes
A function
add_consensus_labels_cell_tablewill run this appending process, with the call inexample_cell_clustering.ipynbplaced at the end of the notebook. The originalcell_table_namewill be overwritten with the same data including the'cell_meta_cluster_rename'column incell_consensus_name(simply'cell_meta_cluster'in the cell table).Users will be able to save multiple times and can also re-run the cell SOM training with the newly-saved cell table if desired.
Additionally, we now allow more flexible locations for the cell table. Initially, it was forced to be in
base_dir. Now, we default the location tosegmentation_dir, with options to change the root. Note that the updated cell table will be saved in the same root directory as the original cell table.