plot.minima3d: Plot minima3d object

In metadynminer3d: Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files from 'Plumed'

Plot minima3d object

Description

'plot.minima3d' plots 3D free energy surface with minima. The free energy surface is plotted the same way as by plot.fes3d with additional minima labels.

Usage

## S3 method for class 'minima3d'
plot(x, xlab = "CV1", ylab = "CV2", zlab = "CV3", level = NULL,
  col = NULL, alpha = NULL, main = NULL, sub = NULL, fill = TRUE, ...)

Arguments

x	minima3d object.
main	an overall title for the plot: see 'title'.
sub	a sub title for the plot: see 'title'.
xlab	a title for the x axis: see 'title'.
ylab	a title for the y axis: see 'title'.
zlab	a title for the z axis: see 'title'.
level	number or numeric vector of levels at which to draw 3D isosurface.
col	color of the free energy surface. It can be a single color or a vector with multiple colors for multiple 3D isosurfaces.
alpha	number or numeric vector of alpha levels (transparency) of 3D isosurfaces.
fill	a logical value indicating whether 3D isosurface is ploted as solid surface (True) or wireframe (False).
...	further arguments passed to or from other methods.

Examples

tfes<-fes(acealanme3d, imax=5000)
minima<-fesminima(tfes)
plot(minima)

metadynminer3d documentation built on April 14, 2022, 5:08 p.m.