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plot_composition_heatmap

Source: R/plot_composition_heatmap.R
plot_composition_heatmap.Rd

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")