add_juxtaview: Generate and add a juxtaview to the current view composition

In saezlab/misty: Multiview Intercellular SpaTial modeling framework

Generate and add a juxtaview to the current view composition

Description

The juxtaview captures the expression of all markers within the immediate neighborhood of a spatial unit.

Usage

add_juxtaview(
  current.views,
  positions,
  neighbor.thr = 15,
  prefix = "",
  cached = FALSE,
  verbose = TRUE
)

Arguments

current.views	the current view composition.
positions	a data.frame, tibble or a matrix with named coordinates in columns and rows for each spatial unit ordered as in the intraview.
neighbor.thr	a threshold value used to indicate the largest distance between two spatial units that can be considered as neighboring.
prefix	a prefix to add to the column names.
cached	a logical indicating whether to cache the calculated view after the first calculation and to reuse a previously cached view if it already exists for this sample.
verbose	a logical controlling the verbosity of the output of the function during execution.

Details

The neighborhood of each spatial unit is estimated by constructing a graph by 2D Delaunay triangulation following by removal of edges with length larger than neighbor.thr. For each spatial unit the juxtaview contains the sum of expressions across its estimated neighbors for each marker.

Value

A mistyR view composition with added juxtaview.

See Also

create_initial_view() for starting a view composition with an intraview only.

Other view composition functions: add_paraview(), add_views(), create_initial_view(), create_view(), remove_views()

Examples

# Create a view composition of an intraview and a juxtaview.

library(dplyr)

# get the expression data
data("synthetic")
expr <- synthetic[[1]] %>% select(-c(row, col, type))
# get the coordinates for each cell
pos <- synthetic[[1]] %>% select(row, col)

# compose
misty.views <- create_initial_view(expr) %>% add_juxtaview(pos, neighbor.thr = 1.5)

# preview
str(misty.views[["juxtaview.1.5"]])

saezlab/misty documentation built on March 25, 2024, 4:11 p.m.