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Change the cell type assignments for each metacell to the ones listed at metacell_types_file.

Usage

update_metacell_types(project, dataset, 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.

Examples

if (FALSE) { # \dontrun{
update_metacell_types("PBMC", "PBMC163k", "raw/metacell-clusters.csv")
} # }