Skip to contents

Plot g_12(r) pair correlation functions for colocalization analysis

Source: R/plot_g12_functions.R
plotG12Functions.Rd

This function creates plots of the inhomogeneous cross pair-correlation function g_12(r) values across different radii for all cell type pairs. It can generate both individual plots for each pair and a combined plot with all pairs overlaid.

Usage

plotG12Functions(
  object,
  r_um_range = c(10, 60),
  pixel_size_um = 1,
  cell_diam_um = 10,
  nsim = 199,
  r_step_um = 2,
  min_points_per_type = 20,
  edge_correction = "translation",
  plot_type = c("combined", "individual", "both"),
  include_confidence = TRUE,
  confidence_level = 0.95,
  colors = NULL,
  line_width = 1.2,
  alpha_bands = 0.3,
  verbose = TRUE
)

Arguments

object

A CoProSingle or CoProMulti object with location and cell type data.

r_um_range

Numeric vector of length 2 specifying the distance range in microns for analysis (default: c(10, 60)).

pixel_size_um

Numeric value specifying microns per coordinate unit. This converts your input coordinates to microns for analysis. For example:

  • If 1 coordinate unit = 50 microns, set pixel_size_um = 50

  • If 1 coordinate unit = 0.325 microns, set pixel_size_um = 0.325

  • If coordinates are already in microns, set pixel_size_um = 1 (default)

cell_diam_um

Numeric value specifying typical cell diameter in microns for intensity smoothing (default: 10).

nsim

Integer specifying number of random labelling simulations for null distribution (default: 199).

r_step_um

Numeric value specifying step size for radius grid in microns (default: 2).

min_points_per_type

Integer specifying minimum number of points required per cell type (default: 20).

edge_correction

Character specifying edge correction method (default: "translation").

plot_type

Character specifying plot type: "combined" for all pairs in one plot, "individual" for separate plots per pair, or "both" (default: "combined").

include_confidence

Logical; whether to include confidence bands from simulations (default: TRUE).

confidence_level

Numeric; confidence level for bands (default: 0.95).

colors

Character vector of colors for different cell type pairs. If NULL, uses default color palette.

line_width

Numeric; width of the g_12(r) lines (default: 1.2).

alpha_bands

Numeric; transparency for confidence bands (default: 0.3).

verbose

Logical; whether to print progress messages (default: TRUE).

Value

A list containing:

  • plot: ggplot object(s) with the g_12(r) plots

  • data: data.frame with g_12(r) values, confidence intervals, and metadata

  • summary: summary statistics for each cell type pair

Details

The function computes the inhomogeneous cross pair-correlation function g_12(r) for each cell type pair and plots the observed values along with confidence bands derived from random labelling simulations.

Values of g_12(r):

  • g_12(r) = 1: Random spatial relationship at distance r

  • g_12(r) > 1: Attraction/colocalization at distance r

  • g_12(r) < 1: Repulsion/segregation at distance r

Examples

if (FALSE) { # \dontrun{
# Basic usage
g12_plots <- plotG12Functions(object)

# Custom parameters with individual plots
g12_plots <- plotG12Functions(object, 
                             r_um_range = c(5, 40),
                             plot_type = "individual",
                             include_confidence = TRUE)

# Access the plot and data
print(g12_plots$plot)
head(g12_plots$data)
} # }