mixing_score_summary: Calculate the (normalised) mixing score for interested cell...

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

Calculate the (normalised) mixing score for interested cell types

Description

Produces a data.frame with mixing scores of input reference and target cells from a SpatialExperiment object. It calculates reference-target interactions and reference-reference interactions based on a radius. It derives the mixing score and the normalised mixing score. Function returns NA if the mixing score is being calculated between cells of the same type.

Usage

mixing_score_summary(
  spe_object,
  reference_celltype,
  target_celltype,
  radius = 20,
  feature_colname
)

Arguments

spe_object	SpatialExperiment object in the form of the output of format_image_to_spe.
reference_celltype	String Vector. Cell types of the reference cells.
target_celltype	String Vector. Cell types of the target cells.
radius	The maximum radius around a reference cell type for another cell to be considered an interaction.
feature_colname	String specifying the column with the desired cell type annotations.

Details

The mixing score was originally defined as the number of immune-tumour interactions divided by the number of immune-immune interactions within a defined radius (Keren et al., 2018). The normalised mixing score normalises the immune-tumour interactions and immune-immune interactions within radius by the total number of immune-tumour and immune-immune interactions in the image, respectively. We have generalized this score to allow calculation of any two cell phenotypes defined by the user.

Value

A data.frame of cell numbers, number of cell interactions, mixing scores, and normalised mixing scores. If there are no reference or target cells found in the image, or there are no reference cells found within the specified radius of any reference cells,the returned (normalised) mixing scores will be NA. If there are no target cells found within the radius of any refernece cells, the returned (normalised) mixing scores will be 0.

Examples

mixing_score_summary(SPIAT::defined_image, reference_celltype = "Tumour", target_celltype="Immune1",
radius = 50, feature_colname = "Cell.Type")

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