Felix Frauhammer

Existing labels

1

Create an object slot where the user can put existing labels (e.g. output from Louvain, reference label transfer, etc.). Write functions to: - manually edit selected clusters. Specifically, a vector...

Function: group_classes (OR logic for rules)

4

Currently all rules are combined with AND, but there might be cases where OR is useful. **Motivation** Use-case 1: For example, markers a1 and a2 might have nice but imperfect...

Using a non-existent parent gives a cryptic error message. Minimal example: `simulated_umis %>% rule("T", "CD3E", ">", 1e-4, parent="oops") %>% plot_classes()` Note that the error only occurs through plot_classes. I think...

Here's code to generate a dot plot of marker genes, given an identity_dataframe. Perhaps add this function to cellpypes package? Usage example: ``` Tsubsets_seurat = data.frame( Th = malt$seurat_clusters %in%...

combine() or similar in name - combines cellpypes objects, which is useful for pseudobulking and setting same thresholds for all samples - makes it easier to compute Differential expression -...

Some classes may have many overlapping cells, it would be nice to visualize this somehow. - How to handle hierarchies? Overlap between parent and child class is obviously a superset-subset...

Currently, my scripts have an obj$embed slot. I would like to change this to obj$embedding (as discussed with Simon on 9th June).