count_cells: Count cells in Seurat object.

In genomics-kl/seurathelpeR: Helper Functions For Seurat V3

Description

count_cells returns a tibble with counts.

Usage

count_cells(seurat_object, group_by_var, subgroup_var)

Arguments

seurat_object	Seurat object.
group_by_var	A character value for grouping the cells. Must correspond to a column in [e-mail].
subgroup_var	Optional parameter. A character value for sub-groups within each group. Must correspond to a column in [e-mail].

Value

Tibble with cell counts and percentages. If subgroup_var is provided, percentages are calculated from the sub-groups making up groups; otherwise, percentages are calculated from the total cell count across the groups.

Examples

# load example dataset from Seurat
data("pbmc_small", package="Seurat")

# Count group-sub-group combinations and calculate % of sub-groups making up groups.
count_cells(pbmc_small, "groups", "RNA_snn_res.0.8")

# Count groups and calculate % of the total that each group consists of.
count_cells(pbmc_small, "groups")

## Not run: 
count_cells(pbmc_small)

## End(Not run)

genomics-kl/seurathelpeR documentation built on Nov. 4, 2019, 1:04 p.m.