plot.profiles: Plot free energy profile

In metadynminer: Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'

Plot free energy profile

Description

'plot.profiles' plots evolution of free energy differences between minima. They are colored by rainbow colors from the global one (blue) to the highest (red).

Usage

## S3 method for class 'profiles'
plot(x, which = NULL, ignoretime = FALSE,
  xlim = NULL, ylim = NULL, main = NULL, sub = NULL, xlab = NULL,
  ylab = NULL, col = NULL, asp = NULL, lwd = 1, axes = T, ...)

Arguments

x	profiles object.
which	vector of indexes of profiles to be plotted (default all).
ignoretime	time in the first column of the HILLS file will be ignored.
xlim	numeric vector of length 2, giving the x coordinates range.
ylim	numeric vector of length 2, giving the y coordinates range.
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'.
col	color code or name, see 'par'.
asp	the y/x aspect ratio, see 'plot.window'.
lwd	line width.
axes	a logical value indicating whether both axes should be drawn on the plot.
...	further arguments passed to or from other methods.

Examples

tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
prof<-feprof(minima)
plot(prof)

metadynminer documentation built on April 14, 2022, 5:06 p.m.