patchSize: Function to compute the area of c3ll patches

In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis

Function to compute the area of c3ll patches

Description

This function constructs polygons around patch cells and computes their area.

Usage

patchSize(
  object,
  patch_name = "patch_id",
  coords = c("Pos_X", "Pos_Y"),
  convex = FALSE
)

Arguments

object	a SingleCellExperiment or SpatialExperiment object
patch_name	single character indicating the colData(object) entry containing the patch cell identifiers.
coords	character vector of length 2 specifying the names of the colData (for a SingleCellExperiment object) or the spatialCoords entries of the cells' x and y locations.
convex	should the convex hull be computed to construct the polygon? Default: the concave hull is computed.

Value

A DataFrame object containing the patch identifier, the constructed polygon and the polygon size.

Author(s)

Nils Eling ([e-mail])

Examples

library(cytomapper)
data(pancreasSCE)

# Build interaction graph
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb", 
                                 type = "expansion", threshold = 20)

# Detect patches of "celltype_B" cells
pancreasSCE <- patchDetection(pancreasSCE, 
                              patch_cells = pancreasSCE$CellType == "celltype_B",
                              expand_by = 5, img_id = "ImageNb",
                              colPairName = "expansion_interaction_graph")
                              
# Compute the patch area
patchSize(pancreasSCE)
  

BodenmillerGroup/imcRtools documentation built on July 1, 2024, 5:15 p.m.