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

In EmSherratt/geomorph: Geometric Morphometric Analyses of 2D/3D Landmark Data

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)

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.

Author(s)

Michael Collyer & Emma Sherratt

See Also

plotRefToTarget, text, text3d

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)

EmSherratt/geomorph documentation built on June 24, 2022, 11:05 p.m.