Set up parameters for grids, points, and links in plotRefToTarget
Function produces a list of parameter changes within plotRefToTarget.
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 = NULL, txt.cex = 0.8, txt.col = "black" )
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 |
txt.adj |
The adjustment value of the landmark label (one or two values, as in base R |
txt.pos |
The position of the landmark label, overrides txt.adj (single numerical value, as in base R |
txt.cex |
The size of the landmark label text (single numerical value, as in base R |
txt.col |
The color of the landmark label text (single numerical value, as in base R |
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.
Michael Collyer & Emma Sherratt
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)
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