get_abundance_info: get_abundance_info

In saeyslab/muscatWrapper: Wrapper functions around muscat for differential expression analysis of multi-sample multi-condition scRNAseq datasets

get_abundance_info

Description

get_abundance_info Visualize cell type abundances. Calculate relative abundances of cell types as well.

Usage

get_abundance_info(
  sce,
  sample_id,
  group_id,
  celltype_id,
  min_cells = 10,
  covariates = NA
)

Arguments

sce	SingleCellExperiment object of the scRNAseq data of interest.
sample_id	Name of the meta data column that indicates from which sample/patient a cell comes from (in sce)
group_id	Name of the meta data column that indicates from which group/condition a cell comes from (in sce)
celltype_id	Name of the column in the meta data of sce that indicates the cell type of a cell.
min_cells	Indicates the minimal number of cells that a sample should have to be considered in the DE analysis. Default: 10. See 'muscat::pbDS'.
covariates	NA if no covariates should be corrected for. If there should be corrected for covariates, this argument should be the name(s) of the columns in the meta data that indicate the covariate(s).

Value

List containing cell type abundance plots and the underlying data frame that was used to make these plots.

Examples

## Not run: 
library(dplyr)
sample_id = "tumor"
group_id = "pEMT"
celltype_id = "celltype"
abundance_info = get_abundance_info(sce = sce, sample_id = sample_id, group_id = group_id, celltype_id =  celltype_id, min_cells = 10)

## End(Not run)

saeyslab/muscatWrapper documentation built on March 11, 2023, 6:14 p.m.