DNE3d: Plot results of a DNE analysis of a surface

Description Usage Arguments Details


plotting function


DNE3d(DNE_File, setRange = c(0, 0), logColors = TRUE, edgeMask = TRUE,
  outlierMask = TRUE, legend = TRUE, legendScale = 1, leftOffset = 1,
  fieldofview = 0)



An object that stores the output of the DNE function


User-defined range for plotting color scheme, see Details


Logical that log transforms the color scheme


Logical that colors edge faces black to indicate their lack of contribution to the total Dirichlet normal energy


Logical that colors outlier faces dark gray to indicate their lack of contribution to the Dirichlet normal energy


Logical indicating whether or not a legend shold be displayed


numeric value setting the relative size of the legend similar in function to cex


numeric value between -1 and 1 setting the degree of offset for the plotted surface to the left. Larger values set further to right.


Passes an argument to par3d changing the field of view in degrees of the resulting rgl


This function creates a heat map on the mesh surface corresponding to the Dirichlet normal energy of each face calculated by the DNE function. Hottest colors represent highest normal energy values

Dirichlet normal energies for the faces of a mesh surface tend to be positively skewed, with a small proportion of the faces contributing much of the total energy for the surface. When logColors is enabled the function colorizes based on the log transformed Dirichlet normal energies, allowing for finer resolution between faces near the mode of the energy per face distribution. Disabling logColors will display the untransformed Dirichlet normal energies.

The legend will update to reflect the other arguments chosen by the user. Colors currently display in the legend in bins, however the colors used in the displayed mesh surface are on a continuum. Ideally, the legend should reflect a continuous stretch of color from the lowest calculated Dirichlet normal energy to the highest. Future versions will adjust the legend to this more intuitive display.

By default, the function sets the lowest Dirichlet normal energy calculated among all faces to a cool color and the highest normal energy calculated among all faces to red, and then colors the remaining faces on a continuous color spectrum between these two end points using either absolute or log transformed Dirichlet normal energy values (depending on the status of logColors). Since the scale is relative to the energies of the input surface, visual comparisons cannot directly be made between multiple plots of different surfaces. The setRange argument allows users to define the minimum and maximum of the plotting color scheme and use it in multiple plots. This enables the direct comparison of different surfaces to one another with red equal to the user-defined maximum and a cool color equal to the user-defined minimum. The user should choose reasonable bounds for the maximum and minimum that are near the maximum and minimum Dirichlet normal energies calculated for their surfaces. setRange will not accept negative values.

The leftOffset value sets how far to the left the surface will appear, intended to help avoid overlap with the legend. Defaults to 0.75.

legendScale sets the relative size of the scale in the same way cex works

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.

Search within the molaR package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.