measure_association_to_cell_properties: measure_association_to_cell_properties

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

measure_association_to_cell_properties

Description

Plots the density or boxplot of a property of two cell celltypes or compares using t test/wilcoxon rank sum test.

Usage

measure_association_to_cell_properties(
  spe_object,
  property = "Cell.Area",
  celltypes,
  feature_colname = "Cell.Type",
  method = "density",
  Nucleus.Ratio = FALSE,
  log.scale = FALSE
)

Arguments

spe_object	SpatialExperiment object in the form of the output of format_image_to_spe.
property	String that is the name of the column of interest.
celltypes	String Vector of celltypes of interest.
feature_colname	String that speficies the column of the cell types.
method	String. The analysis to perform on the selected cell types and property. Options are "density", "box", "t", "wilcox".
Nucleus.Ratio	Boolean whether the ratio of the nucleus size is of interest.
log.scale	Boolean whether to log the data.

Value

With method "box" or "density a plot is returned. With method "t" or "wilcox", the text output from the test are returned.

Examples

measure_association_to_cell_properties(image_no_markers,
                                      celltypes = c("Tumour", "Immune1"),
                                      feature_colname = "Cell.Type",
                                      property = "Cell.Size",
                                      method = "box")
measure_association_to_cell_properties(image_no_markers,
                                      celltypes = c("Tumour", "Immune2"),
                                      feature_colname="Cell.Type",
                                      property = "Cell.Size",
                                      method = "t")

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