vfplots: Plots for visual fields data

In visualFields: Statistical Methods for Visual Fields

Plots for visual fields data

Description

Graphical tools for visualization and statistical analysis of visual fields.

Usage

vfgpar(
  coord,
  tess = vftess(coord),
  probs = c(0, 0.005, 0.01, 0.02, 0.05, 0.95, 0.98, 0.99, 0.995, 1),
  cols = c("#000000", colorRampPalette(c("#FF0000", "#FFFF00"))(4), "#F7F0EB",
    colorRampPalette(c("#00FF00", "#008000"))(4)),
  floor = 0,
  ltprobs = c(0, 0.005, 0.01, 0.02, 0.05, 0.95, 1),
  ltcols = c("#000000", colorRampPalette(c("#FF0000", "#FFFF00"))(4), "#F7F0EB",
    "#008000"),
  gtprobs = c(0, 0.05, 0.95, 0.98, 0.99, 0.995, 1),
  gtcols = c("#000000", "#FF0000", "#F7F0EB", colorRampPalette(c("#00FF00",
    "#008000"))(4)),
  neprobs = c(0, 0.0025, 0.005, 0.01, 0.25, 0.975, 0.99, 0.995, 0.9975, 1),
  necols = c("#000000", colorRampPalette(c("#FF0000", "#FFFF00"))(4), "#F7F0EB",
    colorRampPalette(c("#FFFF00", "#FF0000"))(4)),
  bprobs = c(0, 0.005, 0.01, 0.02, 0.05, 0.95, 0.98, 0.99, 0.995, 1),
  bcols = c("#000000", colorRampPalette(c("#FF0000", "#FFFF00"))(4), "#F7F0EB",
    colorRampPalette(c("#00FF00", "#008000"))(4))
)

vftess(coord, floor = 0, delta = 3)

vfcolscheme(
  probs = c(0, 0.005, 0.01, 0.02, 0.05, 0.95, 0.98, 0.99, 0.995, 1),
  cols = c("#000000", colorRampPalette(c("#FF0000", "#FFFF00"))(4), "#F7F0EB",
    colorRampPalette(c("#00FF00", "#008000"))(4)),
  floor = 0
)

vfprogcolscheme(
  probs = c(0, 0.005, 0.01, 0.02, 0.05, 0.95, 1),
  cols = c("#000000", colorRampPalette(c("#FF0000", "#FFFF00"))(4), "#F7F0EB",
    "#008000")
)

vfplot(vf, type = "td", ...)

vfplotsens(gpar, vf, maxval, digits = 0, ...)

vfplotdev(gpar, vf, dev, devp, digits = 0, ...)

vfplotsdev(gpar, vf, maxval, dev, devp, digits = 0, ...)

vfplotplr(
  vf,
  type = "td",
  alternative = "LT",
  xoffs = 0,
  yoffs = 0,
  addSpark = FALSE,
  thr = 2,
  width = 4,
  height = 2,
  ...
)

vflegoplot(vf, type = "td", grp = 3, ...)

vflegoplotsens(gpar, vfb, vfl, maxb, maxl, crad = 2, digits = 1, ...)

vflegoplotdev(
  gpar,
  vfb,
  devb,
  devpb,
  vfl,
  devl,
  devpl,
  crad = 2,
  digits = 1,
  ...
)

vfsparklines(vf, type = "td", thr = 2, width = 4, height = 2, add = FALSE, ...)

Arguments

coord	print x and y coordinates. Check section Structure of graphical parameters for details
tess	tesselation for the visual field maps. Check section Tesselation in visualFields for details
probs	probability scale to use for TD and PD values. It is a numeric vector of probabilities with values in [0,1]. The values 0 and 1 must be included. Although not technically necessary, it would be best if it is the same as for the normative values used
cols	corresponding colors for each of the probability levels
floor	Flooring value, typically in dB. Default is 0
ltprobs, ltcols	color map for progression with the alternative hypothesis lower than (LT)
gtprobs, gtcols	color map for progression with the alternative hypothesis lower than (GT)
neprobs, necols	color map for progression with the alternative hypothesis not equal (NE)
bprobs, bcols	color map for progression with blth alternative hypotheses LT and GT (B for both)
delta	Distance over which the boundary should be shifted. See for polyclip
vf	the visual fields data to plot
type	the type of data to plot: sensitivities ('s'), total deviation values ('td'), pattern deviation values ('pd'), a hybrid plot that shows sensitivity grayscale with TD values and corresponding probability levels ('tds'), or PD values and corresponding probability levels ('pds'). Default is 'td'.
...	other graphical arguments. See plot
gpar	graphical parameters
maxval	maximum value, typically in dB, for the generation of a grayscale
digits	digits to round values to plot. Default is 0
dev	deviation (TD or PD) values
devp	deviation (TD or PD) probability values
alternative	alternative hypothesis used in progression analyses. Allowed values are 'LT' (as in "lower than", default), 'GT' (as in "greater than"), 'NE' (as in "not equal"), and 'both' (both 'LT' and 'GT')
xoffs, yoffs	offset x and y where to print the slope values. That is, the distance from the center of each Voronoy polygons in degrees of visual angle
addSpark	whether to overlay a sparkline graph in each visual field location. The parameters thr, width, and height are used only if addSpark is TRUE. Default value is FALSE.
thr	threshold used for the median absolute deviation of residuals from simple linear regression. If greater than the threshold, the sparkline for that location is plotted in red and with a thicker line. Default is '2' (dB)
width	the width of each pointwise sparkline plot. Default is '4' (degrees of visual angle)
height	the height of each pointwise sparkline plot. Default is '2' (degrees of visual angle)
grp	number of baseline (first) and last visual fields to group. Default is '3'
vfb	baseline visual field data
vfl	last visual field data
maxb	maximum value for the grayscale at baseline visual field data
maxl	maximum value for the grayscale for last visual field data
crad	radius of the circle in the legoplot
devb	baseline visual field (TD or PD) deviation values
devpb	baseline visual field (TD or PD) deviation probability values
devl	last visual field (TD or PD) deviation values
devpl	last visual field (TD or PD) deviation probability values
add	whether to generate a new plot ('FALSE', as default) or to add to an existing figure ('TRUE')

Details

The following functions generate plots using visual fields data

• vfgpar generates simple graphical parameters

• vftess generates a structure to handle the visual field tessellation. Check section Tesselation in visualFields below for further details

• vfcolscheme generates the structures to handle the color scheme Check section Color schemes in visualFields below for further details

• vfprogcolscheme generates the structures to handle the color scheme for progression analysis. Check section Color schemes in visualFields below for further details

• vfplot plots a single test for visual field data

• vfplotsens plots a single test for visual field sensitivity data with a grayscale where darker means greater sensitivity loss

• vfplotdev plots a single test for visual field total or pattern deviation data with probability scales represented in color

• vfplotplr plots the results of pointwise linear regression for a series of visual fields for an eye from a subject

• vflegoplot the legoplot shows the differences between the average values of visual field tests taken as baseline and those at the end of follow up

• vflegoplotsens the legoplot for visual field sensitivity data with a grayscale where darker means greater sensitivity loss

• vflegoplotdev the legoplot for visual field total or pattern deviation data with probability scales represented in color

• vfsparklines the sparklines graph shows spark lines for the series of visual field sensitivities, or total or pattern deviation data for each location

Value

vfgpar returns a list with graphical parameters to be used for vfplots

vftess returns a list with the xlim, ylim, tessellation tiles and an outer hull to be used for vfplots

vfcolscheme returns a list with a lookup table and a function that define the color scheme to be used for vfplots

vfprogcolscheme returns the default vfcolscheme to be used for vfplots

vfplot No return value

vfplotsens No return value

vfplotdev No return value

vfplotsdev No return value

vfplotplr No return value

vflegoplot No return value

vflegoplotsens No return value

vflegoplotdev No return value

vfsparklines No return value

Structure of graphical parameters

Graphical parameters for visualFields must be a list containing

• coord print x and y coordinates. They could be different from the the real visual field location testing coordinates in complex visual field grids to help readability and improve visualization of statistical results

• tess tesselation for the visual field maps. Check section Tesselation in visualFields

• colmap color map representing the probability scale. Check section Color schemes in visualFields

A default graphical parameters can be generated with generategpar

Tesselation in visualFields

A tesselation in visualFields must be defined with a list containing

• xlim,

• ylim 2-dimensional vectors containing the minimum and maximum x and y values

• floor the value to be assinged to any sensitivity value lower than floor

• tiles a list of as many tiles defining the tesselation as visual field test locations. Each element of the list is a table with x and y coordinates defining a polygon containing the corresponding test location. Each polygon is thus the tile for each visual field test location

• hull a table with x and y coordinates defining the outer hull of the tessellation

A default tessellation can be generated with vftess

Color schemes in visualFields

A color scheme in visualFields must be defined with a list containing

• map a table mapping probabilities levels with colors defined in hexadecimal base

• fun a function that takes sensitivity values and deviation probability levels and returns the corresponding color code.

A default color scheme can be generated with vfcolscheme

Examples

# generate a structure with default graphical parameters for the 30-2 map
vfgpar(locmaps$p30d2$coord)
# generate a structure with default tesselation for the 30-2 map
vftess(locmaps$p30d2$coord)
# default color scheme
vfcolscheme()
# default color scheme for progression
vfprogcolscheme()
# plot visual field values for the last field in the series for the first
# subject in the dataset vfpwgSunyiu24d2
# grayscale with sensitivity values
vfplot(vfselect(vffilter(vfpwgRetest24d2, id == 1), n = 1), type = "s")
# TD values
vfplot(vfselect(vffilter(vfpwgRetest24d2, id == 1), n = 1), type = "td")
# PD values
vfplot(vfselect(vffilter(vfpwgRetest24d2, id == 1), n = 1), type = "pd")
# hybrid sensitivities and TD values
vfplot(vfselect(vffilter(vfpwgRetest24d2, id == 1), n = 1), type = "tds")
# hybrid sensitivities and PD values
vfplot(vfselect(vffilter(vfpwgRetest24d2, id == 1), n = 1), type = "pds")
# plot results from pointwise linear regression for the series of
# visual fields for the right eye in the dataset vfpwgSunyiu24d2
# with sensitivity values
vfplotplr(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "s")
# TD values
vfplotplr(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "td")
# PD values
vfplotplr(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "pd")
# legoplot for the series of visual fields for the right eye
# of the subject in the dataset vfpwgSunyiu24d2
# with sensitivity values
vflegoplot(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "s")
# TD values
vflegoplot(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "td")
# PD values
vflegoplot(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "pd")
# sparklines for the series of visual fields for the right eye of
# the subject in the dataset vfpwgSunyiu24d2
# with sensitivity values
vfsparklines(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "s")
# TD values
vfsparklines(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "td")
# PD values
vfsparklines(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "pd")

visualFields documentation built on March 18, 2022, 7:14 p.m.