PlotAdjacency {womblR}

PlotAdjacency

Description

Plots a heat map of the differential light sensitivity on the Humphrey Field Analyzer-II visual field.

Usage

PlotAdjacency(
  Wij,
  Visit = 1,
  stat = "mean",
  main = "Estimated Adjacencies",
  color.scheme = c("Black", "White"),
  edgewidth = 2,
  cornerwidth = 1/4,
  lwd.border = 3,
  color.bs = "gray",
  zlim = c(0, 1),
  legend = TRUE,
  DM = NULL,
  W = NULL
)

Arguments

Wij

a PosteriorAdj object.

Visit

either an integer (1,...,Nu) indicating the visit number for which you want to get the adjacencies to plot or NA. If NA, then the plot will produce the dissimilarity metric at each adjacency.

stat

either "mean" or "sd" (only used for Visit != NA).

main

an overall title for the plot.

color.scheme

a vector of colors to be used to show the adjacencies changing.

edgewidth

a scalar indicating the width of the edges.

cornerwidth

a scalar indicating the width of the corners.

lwd.border

a scalar indicating width of the visual field border.

color.bs

one color specifying the blind spot.

zlim

the limits used for the legend (default are c(0,1)).

legend

logical, indicating whether the legend should be present (default = TRUE).

DM

a dissimilarity metric to be plotted at each location on the visual field (default = NULL).

W

an adjacency matrix that specifies the visual field, required if Wij is not provided (default = NULL).

Details

PlotAdjacency is used in the application of glaucoma progression to plot the posterior mean and standard deviation neighborhood adjacencies across the visual field.

Author(s)

Samuel I. Berchuck

Examples

###Define blind spot locations on the HFA-II
blind_spot <- c(26, 35)

###Load visual field adjacency matrix
W <- HFAII_Queen[ -blind_spot, -blind_spot]

###Load Garway-Heath angles for dissimiliarity metric
DM <- GarwayHeath[-blind_spot] #Uses Garway-Heath angles object "GarwayHeath"

###Adjacency plots
PlotAdjacency(W = W, DM = DM, zlim = c(0, 180), Visit = NA,
              main = "Garway-Heath dissimilarity metric\n across the visual field")