visualFields (version 0.5.4)

vfplot2_poplr: plot with the PoPLR analysis

Description

plots the slope values and the corresponding probabiliby category for each location

Usage

vfplot2_poplr( sl, pval, vfinfo, newWindow = FALSE, txtfont = "mono",
              pointsize = 7, width = 6,
              xminmax = 29, yminmax = 29,
              outerSymbol = "circles", innerSymbol = "circles",
              outerSize = 1, innerSize = 1,
              outerInch = 0.24, innerInch = 0.12,
              lengthLines = 0, thicknessLines = 0,
              colorMapType = "pval", colorScale = NULL,
              ringMapType  = NULL, ringScale  = NULL,
              imparedVision = 10, borderThickness = 2,
              idxNotSeen = NULL, rangeNormal = NULL,
              conormal = NULL )

Arguments

sl

slopes

pval

pvalues calculated for the slope

vfinfo

information about the visual field

newWindow

boolean value- TRUE will generate a new window for the plot. Default value is TRUE

txtfont

font of the text with visual-sensitivity values. Default is mono

pointsize

size of the text with visual-sensitivity values. Default is 7

width

width of the window. height is calucated using the width, xminmax and yminmax

xminmax

minimum and maximum limits on the x axis

yminmax

minimum and maximum limits on the y axis

outerSymbol

The outer symbol at all locations. Can be any of circles, squares, rectangles, stars. Default is circle

innerSymbol

The inner symbol at all locations. Can be any of circles, squares, rectangles, stars. Default is circle

outerSize

Relative size of the outer symbol. Default is 1

innerSize

Relative size of the inner symbol. Default is 1

outerInch

Maximum size of the outer symbol in inches. Default is 0.2

innerInch

Maximum size of the inner symbol in inches. Default is 0.1

lengthLines

length of the lines denoting the orientation of the RNF bundle

thicknessLines

thickness of the lines denoting the orientation of the RNF bundle

colorMapType

what does color map categorizes. It can be pvals, slopes, or years blind. Default is pvals

colorScale

Color mapping to use. Default is NULL. A different default is given depending on colorMapType

ringMapType

what concentric rings categorizes. It can be pvals or slopes, or years blind. Default is NULL, for which no rings are shown.

ringScale

Ring mapping to use. Default is NULL. A different default is given depending on ringMapType

imparedVision

sensitivity below which it is considered imparement. Default is 10

borderThickness

Thickness of the borders if ringMapType is not NULL. Default is 5

idxNotSeen

index of locations that are not seen. These locations will be displayed with a solid balck circle. Default is NULL.

rangeNormal

range to indicate which slopes are normal. All significance from data points within the range will be removed. Default is NULL.

conormal

if a rangeNormal is defined, then this specifies the within-normal category. Default is NULL. If colorMapType = "pval", then it is 95, if colorMapType = "slope", then it is 0.5

Details

The vfplot function operates on a single row of visual fileds (vf). Depending on the plot type it will generate a plot representing the sensitivity at each location. The color scheme elucidates the degree of sensitivity at that location. Locations with zero sensitivity are shown in black. Blind spots have been excluded fronm the plot

References

[1] N. O'Leary, B. C. Chauhan, and P. H. Artes. Visual field progression in glaucoma: estimating the overall significance of deterioration with permutation analyses of pointwise linear regression (PoPLR). Investigative Ophthalmology and Visual Science, 53, 2012

See Also

poplr, hist_poplr, poplr_cstat, poplr_pstat, vflayout2_poplr

Examples

# NOT RUN {
  res <- poplr( vf91016right )
  vfplot2_poplr( res$sl, res$pval, res$vfdata )
# }