plot_composition_heatmap: plot_composition_heatmap

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

plot_composition_heatmap

Description

Produces a heatmap showing the marker percentages within each cluster and the cluster sizes.

Usage

plot_composition_heatmap(
  composition,
  pheno_to_exclude = NULL,
  log_values = FALSE,
  feature_colname
)

Arguments

composition	Data.frame. Output from composition_of_neighborhoods.
pheno_to_exclude	String Vector of phenotype to exclude.
log_values	Boolean. TRUE if the percentages should be logged (base 10).
feature_colname	String. Column with cell types.

Value

A plot 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")
plot_composition_heatmap(neighborhoods_vis, feature_colname="Cell.Type")

TrigosTeam/SPIAT documentation built on Aug. 22, 2024, 7:50 p.m.