plot_cell_categories: plot_cell_categories

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

plot_cell_categories

Description

Produces a scatter plot of the cells of their x-y positions in the tissue. Cells are coloured categorically by phenotype. Cells not part of the phenotypes of interest will be coloured "lightgrey".

Usage

plot_cell_categories(
  spe_object,
  categories_of_interest = NULL,
  colour_vector = NULL,
  feature_colname = "Cell.Type",
  cex = 1,
  layered = FALSE
)

Arguments

spe_object	SpatialExperiment object in the form of the output of format_image_to_spe.
categories_of_interest	Vector of cell categories to be coloured.
colour_vector	Vector specifying the colours of each cell phenotype.
feature_colname	String specifying the column the cell categories belong to.
cex	Numeric. The size of the plot points. Default is 1.
layered	Boolean. Whether to plot the cells layer by layer (cell categories). By default is FALSE.

Value

A plot is returned

Examples

categories_of_interest <- c("Tumour", "Immune1","Immune2","Immune3")
colour_vector <- c("red","darkblue","blue","darkgreen")
plot_cell_categories(SPIAT::defined_image, categories_of_interest, colour_vector,
feature_colname = "Cell.Type")

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