Morpho: checkLM – R documentation

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checkLM

Visually browse through a sample rendering its landmarks and corresponding surfaces.

Description

Browse through a sample rendering its landmarks and corresponding surfaces. This is handy e.g. to check if the landmark projection using placePatch was successful, and to mark specific specimen.

Usage

checkLM(dat.array, path = NULL, prefix = "", suffix = ".ply",
  col = "white", pt.size = NULL, alpha = 1, begin = 1,
  render = c("w", "s"), point = c("s", "p"), add = FALSE,
  meshlist = NULL, Rdata = FALSE, atlas = NULL, text.lm = FALSE)

Arguments

`dat.array`	array or list containing landmark coordinates.
`path`	optional character: path to files where surface meshes are stored locally. If not specified only landmarks are displayed.
`prefix`	prefix to attach to the filenames extracted from `dimnames(dat.array)[[3]]` (in case of an array), or `names(dat.array)` (in case of a list)
`suffix`	suffix to attach to the filenames extracted from `dimnames(dat.array)[[3]]` (in case of an array), or `names(dat.array)` (in case of a list)
`col`	mesh color
`pt.size`	size of plotted points/spheres. If `point="s"`. `pt.size` defines the radius of the spheres. If `point="p"` it sets the variable `size` used in `point3d`.
`alpha`	value between 0 and 1. Sets transparency of mesh 1=opaque 0= fully transparent.
`begin`	integer: select a specimen to start with.
`render`	if render="w", a wireframe will be drawn, else the meshes will be shaded.
`point`	how to render landmarks. "s"=spheres, "p"=points.
`add`	logical: add to existing rgl window.
`meshlist`	list holding meshes in the same order as `dat.array` (Overrides `path`).
`Rdata`	logical: if the meshes are previously stored as Rdata-files by calling save(), these are simply loaded and rendered. Otherwise it is assumed that the meshes are stored in standard file formats such as PLY, STL or OBJ, that are then imported with the function `file2mesh`.
`atlas`	provide object generated by `createAtlas` to specify coloring of surface patches, curves and landmarks
`text.lm`	logical: number landmarks. Only applicable when `atlas=NULL`.

Value

returns an invisible vector of indices of marked specimen.

Note

if Rdata=FALSE, the additional command line tools need to be installed (http://sourceforge.net/projects/morpho-rpackage/files/Auxiliaries/)

Examples

data(nose)
###create mesh for longnose
longnose.mesh <- tps3d(shortnose.mesh,shortnose.lm,longnose.lm,threads=1)
### write meshes to disk
save(shortnose.mesh, file="shortnose")
save(longnose.mesh, file="longnose")

## create landmark array
data <- bindArr(shortnose.lm, longnose.lm, along=3)
dimnames(data)[[3]] <- c("shortnose", "longnose")
## Not run: 
checkLM(data, path="./",Rdata=TRUE, suffix="")

## End(Not run)

## now visualize by using an atlas:
atlas <- createAtlas(shortnose.mesh, landmarks =
           shortnose.lm[c(1:5,20:21),],
patch=shortnose.lm[-c(1:5,20:21),])
## Not run: 
checkLM(data, path="./",Rdata=TRUE, suffix="", atlas=atlas)

## End(Not run)
## remove data from disk
unlink("shortnose")
unlink("longnose")

Morpho

Calculations and Visualisations Related to Geometric Morphometrics

v2.8

GPL-2

Authors

Stefan Schlager [aut, cre, cph], Gregory Jefferis [ctb], Dryden Ian [cph]

Initial release

2020-02-26