gridPar: Set up parameters for grids, points, and links in plotRefToTarget

Description

Function produces a list of parameter changes within plotRefToTarget.

Usage

gridPar(
  pt.bg = "gray",
  pt.size = 1.5,
  link.col = "gray",
  link.lwd = 2,
  link.lty = 1,
  out.col = "gray",
  out.cex = 0.1,
  tar.pt.bg = "black",
  tar.pt.size = 1,
  tar.link.col = "black",
  tar.link.lwd = 2,
  tar.link.lty = 1,
  tar.out.col = "black",
  tar.out.cex = 0.1,
  n.col.cell = 20,
  grid.col = "black",
  grid.lwd = 1,
  grid.lty = 1,
  txt.adj = NULL,
  txt.pos = 2,
  txt.cex = 0.8,
  txt.col = "black"
)

Arguments

pt.bg: Background color of reference configuration points (single value or vector of values)
pt.size: Scale factor for reference configuration points (single value or vector of values)
link.col: The color of links for reference configurations (single value or vector of values)
link.lwd: The line weight of links for reference configurations (single value or vector of values)
link.lty: The line type of links for reference configurations (single value or vector of values)
out.col: The color of outline for reference configurations (single value or vector of values)
out.cex: The size of plotting symbol of outline for reference configurations (single value or vector of values)
tar.pt.bg: Background color of target configuration points (single value or vector of values)
tar.pt.size: Scale factor for target configuration points (single value or vector of values)
tar.link.col: The color of links for target configurations (single value or vector of values)
tar.link.lwd: The line weight of links for target configurations (single value or vector of values)
tar.link.lty: The line type of links for target configurations (single value or vector of values)
tar.out.col: The color of outline for target configurations (single value or vector of values)
tar.out.cex: The size of plotting symbol of outline for target configurations (single value or vector of values)
n.col.cell: The number of square cells (along x axis) for grids (single numerical value)
grid.col: The color of grid lines (single value)
grid.lwd: Scale factor for the weight of grid lines (single numerical value)
grid.lty: The line type for grid lines (single numerical value, as in base R plot)
txt.adj: The adjustment value of the landmark label (one or two values, as in base R text and text3d)
txt.pos: The position of the landmark label, overrides txt.adj (single numerical value, as in base R text and text3d)
txt.cex: The size of the landmark label text (single numerical value, as in base R text and text3d)
txt.col: The color of the landmark label text (single numerical value, as in base R text and text3d)

Author

Michael Collyer & Emma Sherratt

Details

The function allows users to vary certain plotting parameters to produce different graphical outcomes for plotRefToTarget. Not all parameters need to be adjusted to use this function, as the defaults above will be used.

Examples

Run this code

if (FALSE) {
data(plethodon) 
Y.gpa <- gpagen(plethodon$land)    #GPA-alignment
ref <- mshape(Y.gpa$coords)
plotRefToTarget(ref, Y.gpa$coords[,,39]) # default settings

# Altering points and links
GP1 <- gridPar(pt.bg = "red", pt.size = 1, link.col = "blue", link.lwd = 2, 
n.col.cell = 50)
plotRefToTarget(ref, Y.gpa$coords[,,39], gridPars = GP1, mag = 2, 
links = plethodon$links, method = "TPS")

# Altering point color
GP2 <- gridPar(pt.bg = "green", pt.size = 1) 
plotRefToTarget(ref, Y.gpa$coords[,,39], gridPars = GP2, mag = 3, 
method = "vector")

# Altering ref and target points
GP3 <- gridPar(pt.bg = "blue", pt.size = 1.5, tar.pt.bg = "orange", 
tar.pt.size = 1) 
plotRefToTarget(ref, Y.gpa$coords[,,39], gridPars = GP3, mag = 3, 
method = "points")

# Altering outline color
GP4 <- gridPar(tar.out.col = "red", tar.out.cex = 0.3) 
plotRefToTarget(ref, Y.gpa$coords[,,39], gridPars = GP4, mag = 3, 
outline = plethodon$outline, method = "TPS")

# Altering text labels
GP5 <- gridPar(txt.pos = 3, txt.col = "red") 
plotRefToTarget(ref, Y.gpa$coords[,,39], gridPars = GP5, mag = 3, 
method = "vector", label = TRUE)
}