Heatmap of cell-cell connections — plot_cell_connections • TopKAT

Visualize the connectivity matrix produced by generate_connectivity

Usage

plot_cell_connections(image, threshold, title, type.column, unique.types)

Arguments

image: A data.frame containing the image information.
threshold: Radius to plot, usually threshold generated by scale_importance
title: Plot title
type.column: The name of the column in images.df that contains the cell types
unique.types: Vector of unique cell types in the type.column

Value

Returns a ggplot of the heatmap of cell-cell connections.

Examples

require(magrittr)
plot_cell_connections(
   image = data1.df %>% dplyr::filter(PID == 1),
   threshold = 10,
   title = "",
   type.column = "type",
   unique.types = unique(data1.df$type)
)