Change the cell type assignments for each metacell to the ones listed at metacell_types_file.
Arguments
- project
path to the project directory
- dataset
name for the dataset, e.g. "PBMC"
- metacell_types_file
path to a tabular file (csv,tsv) with cell type assignement for each metacell. The file should have a column named "metacell" with the metacell ids and another column named "cell_type" or "cluster" with the cell type assignment. Metacell ids that do not exists in the data would be ignored.
Details
This is usually done after a first iteration of annotation using the "Annotate" tab in the MCView annotation, which can export a valid metacell_types_file.
The file should have a column named "metacell" with the metacell ids and another
column named "cell_type" or "cluster" with the cell type assignment.
Note that the exported file from the __MCView__ app contains additional fields which will be ignored in this function.
Under the hood - MCView updates a file named "metacell_types.tsv" under project/cache/dataset, which can also be edited manually.
If the file contains an additional 'color' field, the cell type colors would be updated as well.