vfplots: Plots for visual fields data

Description Usage Arguments Details Value Structure of graphical parameters Tesselation in visualFields Color schemes in visualFields Examples

Description

Graphical tools for visualization and statistical analysis of visual fields.

Usage

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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, ...)

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,
  ...
)

vfplotsparklines(
  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

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

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)

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

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

vfplotsparklines No return value

Structure of graphical parameters

Graphical parameters for visualFields must be a list containing

A default graphical parameters can be generated with generategpar

Tesselation in visualFields

A tesselation in visualFields must be defined with a list containing

A default tessellation can be generated with vftess

Color schemes in visualFields

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

A default color scheme can be generated with vfcolscheme

Examples

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# 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
vfplotsparklines(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "s")
# TD values
vfplotsparklines(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "td")
# PD values
vfplotsparklines(vffilter(vfpwgSunyiu24d2, eye == "OD"), type = "pd")

visualFields documentation built on Aug. 17, 2021, 1:06 a.m.