RFI3d {molaR}

Plot 3D and 2D areas of a mesh used to calculate relief index

Description

A function that plots a three-dimensional model of the mesh surface and includes a footprint of the two-dimensional area for visual comparison.

Usage

RFI3d(
  RFI_File,
  displacement = -1.9,
  SurfaceColor = "gray",
  FootColor = "red",
  FootPts = FALSE,
  FootPtsColor = "black",
  Opacity = 1,
  legend = F,
  main = "",
  cex = 1,
  leftOffset = 0,
  fieldofview = 0,
  fileName = NA,
  binary = FALSE
)

Arguments

RFI_File

An object that stores the output of the RFI function

displacement

Numeric that moves the surface footprint some proportion of the height of the mesh. 0 is in the vertical center of the surface, negative values displace the footprint downward.

SurfaceColor

String that controls the color of the 3D surface mesh

FootColor

String that controls the color of the 2D surface footprint

FootPts

Logical indicating whether to plot the flattened points of the footprint from the original ply file

FootPtsColor

Color of the plotted footprint points if FootPts = TRUE

Opacity

Numeric that adjusts the opacity of the 3D mesh surface

legend

Logical indicating whether or not to include a legend of the colors chosen to represent the 3D surface and footprint

main

String indicating plot title

cex

Numeric setting the relative size of the legend and title

leftOffset

Numeric between -1 and 1 setting the amount of offset for the plotted surface to the left. Larger values push surface farther to right.

fieldofview

Passes an argument to par3d() changing the field of view in degrees of the resulting surface plot

fileName

String indicating a name to save the plotted surface to as a *.ply file; default of 'NA' will not save a file

binary

Logical indicating whether or not the saved surface plot should be binary, passed to vcgPlyWrite()

Details

This function can help to visualize the three-dimensional and two dimensional areas that are used in calculating the relief index of a surface by displaying both at the same time. The RFI function must be performed first.

Opacity can be adjusted in a range from fully opaque (1) to fully transparent (0) in order to help visualize the footprint. The vertical placement of the footprint along the Z axis can be altered with displacement, depending on how the user wishes to view the surface, or on the original mesh orientation.

A title can be added to the plot by supplying a character string to the main argument. Title and legend size are controlled with the cex argument, analogous to that in the default R graphics device.

The leftOffset value sets how far to the left the surface will plot, intended to help avoid overlap with the legend. Value of 0 will center the surface and should be invoked if the legend argument is disabled. Higher values will push the surface farther left and negative values will push it to the right. It is recommended that these values be restricted between -1 and 1 to avoid plotting the surface outside of the rgl window.

fieldofview is set to a default of 0, which is an isometric projection. Increasing it alters the degree of parallax in the perspective view, up to a maximum of 179 degrees (see rgl::par3d()).

The plotted, colorized surface can be saved as a *.ply to the working directory by changing the fileName argument from NA to a string (e.g., "RFIPlot"). The resultant ply file can be opened and manipulated in other 3D visualizing programs, such as MeshLab, but will NOT retain its legend (a background of the plotting window). To retain the legend, the user is encouraged to utilize the function 'snapshot3d()' in the rgl package. (see rgl::rgl.snapshot()) The binary argument saves a file in ascii format by default, which is supported by more 3D visualization software than is binary. However, binary files will be considerably smaller.

Examples

RFI_File <- RFI(Tooth, alpha=0.5)
RFI3d(RFI_File)