Import cell metadata to an MCView dataset — import_cell

Import metadata which is at the cell level to MCView. The metadata can be summarised to the metacell level by setting summarise_md to TRUE, in which case it could be shown at the "Genes" and "Markers" tabs. In order to view data at the samples level, an additional sample identifier should be given as a column named "samp_id" in the cell_metadata data frame.

Usage

import_cell_metadata(
  project,
  dataset,
  cell_metadata,
  cell_to_metacell = NULL,
  summarise_md = FALSE,
  add_samples_tab = TRUE,
  ...
)

Arguments

project

path to the project

dataset

name for the dataset, e.g. "PBMC". The name of the dataset can only contain alphanumeric characters, dots, dashes and underscores.

cell_metadata

data frame with a column named "cell_id" with the cell id and other metadata columns, or a name of a delimited file which contains such data frame. For activating the "Samples" tab, the data frame should have an additional column named "samp_id" with a sample identifier per cell (e.g., batch id, patient etc.). Optionally, a column named "metacell" can be added to the data frame, which will be used instead of the cell_to_metacell parameter.

cell_to_metacell

data frame with a column named "cell_id" with cell id and another column named "metacell" with the metacell the cell is part of, or a name of a delimited file which contains such data frame. If NULL, the metacell will be inferred from the 'metacell' column in cell_metadata.

summarise_md

summarise cell metadata to the metacell level.

add_samples_tab

add the 'Samples' tab to the config file if it doesn't exist

...

Arguments passed on to cell_metadata_to_metacell

func: summary function for the cell metadata for non categorical metadata columns (e.g. mean, median, sum)
categorical: a vector with names of categorical variables. The returned data frame would have a column for each category where the values are the fraction of cells with the category in each metacell.