Calculates the number and proportion of each cell type.
Usage
calculate_cell_proportions(
sce_object,
reference_celltypes = NULL,
celltypes_to_exclude = NULL,
feature_colname = "Phenotype",
plot.image = TRUE
)
Arguments
- sce_object
SingleCellExperiment object in the form of the output of
format_image_to_sce
.- reference_celltypes
String Vector specifying reference cell types. If NULL (default), then the proportion of each cell type against all cells is returned. Alternatively, a custom vector of cell types can be used as input, and these will be used as the denominator in the calculation of the proportions.
- celltypes_to_exclude
String Vector specifying cell types to exclude. For example "OTHER" will exclude that celltype from the Total. If NULL, all cell types are included.
- feature_colname
String. Column of cells to choose the cell type from (e.g. Phenotype, Cell.Type, etc).
- plot.image
Boolean. Whether to plot the barplot of the cell percentages. By default is TRUE.
Examples
calculate_cell_proportions(SPIAT::defined_image, reference_celltypes = NULL,
celltypes_to_exclude = "Others", feature_colname="Cell.Type", plot.image = FALSE)
#> Cell_type Number_of_celltype Proportion Percentage Proportion_name
#> 5 Tumour 819 0.41679389 41.679389 /Total
#> 3 Immune3 630 0.32061069 32.061069 /Total
#> 1 Immune1 338 0.17201018 17.201018 /Total
#> 2 Immune2 178 0.09058524 9.058524 /Total