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kanaverse
Feature request: Re-analysing a user-specified subset of data
It would be great if it were possible to select a subset of cells and re-analyse that subset. E.g., In a dataset of PBMCs, select all 'B cells' (based on the cluster annotations) and re-analyse to look for subclusters within the B cell population. Is this something planned for future release or that would be feasible to implement?
that's a great idea. we could enable this by making the cluster names clickable and automatically open a new session with this subset.
What really happens in the background is the app would subset the cells in that cluster, create a new h5ad and store this in the browser. Tracking the provenance of datasets and subsets is left to the user.
Awesome! Thank you for considering the suggestion and for making such a great app.
It took a while, but we accidentally added this feature as a combination of other features.
The workflow goes like this:
- Do an analysis on the full dataset.
- Save the results as ZIP file.
- Start a new analysis (possibly on a different tab, if you want to look at both at once), loading the aforementioned ZIP file.
- Click on "subsetting by annotation" and choose what you want to subset by.
This allows you to subset by cluster numbers or custom selections (choose 1 for cells inside the selection). And of course, you can pick any of your existing annotations if you want.
Admittedly, this isn't the streamlined experience I was thinking about in #120, but I would argue that this approach is more transparent and reproducible, as the user is obliged to save a copy of the original analysis. If we just added an "analyze subset" button directly, kana would have to keep track of the provenance of the subsets - tracking how they were generated in the configuration, invalidating them if the parent analysis changes, saving them in the results, etc...
Thanks!
If someone has a processed dataset in another format (e.g., .rds containing a SingleCellExperiment object) can they go directly to loading it and "subsetting by annotation"?
