composition_of_neighborhoods

Returns a data.frame which contains the percentages of cells with a specific marker within each neighborhood. and the number of cells in the neighborhood.

Usage

composition_of_neighborhoods(neighborhoods_df, feature_colname)

Arguments

neighborhoods_df

Data.frame that is the output of identify_neighborhoods.

feature_colname

String. Column with cell types.

Value

A data.frame is returned

Examples

neighborhoods <- identify_neighborhoods(image_no_markers, method = "hierarchical",
min_neighborhood_size = 100, cell_types_of_interest = c("Immune", "Immune1", "Immune2"),
radius = 50, feature_colname = "Cell.Type")

neighborhoods_vis <- composition_of_neighborhoods(neighborhoods, feature_colname="Cell.Type")