geomorph (version 3.0.3)

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 = 0.5, txt.pos = 1, 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)

txt.pos

The position of the landmark label (single numerical value, as in base R text)

txt.cex

The size of the landmark label text (single numerical value, as in base R text)

txt.col

The color of the landmark label text (single numerical value, as in base R text)

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.

See Also

plotRefToTarget

Examples

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)