update_metacell_types: Update cell type assignment for each metacell

In tanaylab/MCView: A Shiny App for Metacell Analysis

Update cell type assignment for each metacell

Description

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

## Not run: 
update_metacell_types("PBMC", "PBMC163k", "raw/metacell-clusters.csv")

## End(Not run)

tanaylab/MCView documentation built on June 1, 2025, 8:08 p.m.