monogeneaGM (version 1.1)

polyVis: Wireframe plot of monogenean anchor

Description

This function plots the ventral and dorsal anchors as polygons in their natural positions on the specimen slide.

Usage

polyVis(index, spacing = 250, havelist = FALSE, listdata = NULL, tit = "")

Arguments

index

the index of a (tps) text file or matrix containing the (eleven) landmark coordinates in the following order: right ventral, left ventral, right dorsal, left dorsal

spacing

a numeric constant specifying the spacing on the x and y coordinates relative to slide center

havelist

choose TRUE if the landmark coordinate data are contained in a list

listdata

a list containing objects that are matrices of 44 rows and 2 columns containing raw landmark coordinate data

tit

title for the plot

Details

This plot is useful for detecting slides with inconsistencies in magnification. It is also useful for detecting poor quality samples, as indicated by large shape variation between left and right forms.

References

Khang TF, Soo OYM, Tan WB, Lim LHS. (2016). Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution. PeerJ 4:e1668.

Examples

data(ligophorus_tpsdata)
#Simultaneously visualise the first four specimen slides
par(mfrow=c(2,2))
par(mar=c(3,3,2,1.5))
mapply(function(k) polyVis(k, spacing=300, havelist=TRUE,
listdata=ligophorus_tpsdata$grandis), k=1:4)