plot.fes: Plot free energy surface object

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

Plot free energy surface object

Description

'plot.fes' plots free energy surface. For a fes with one collective variable it plots a 1D profile. For a fes with two collective variables it plots 2D free energy surface using image, contours or combination of both (default).

Usage

## S3 method for class 'fes'
plot(x, plottype = "both", colscale = F, xlim = NULL,
  ylim = NULL, zlim = NULL, main = NULL, sub = NULL, xlab = NULL,
  ylab = NULL, nlevels = 10, levels = NULL,
  col = rainbow(135)[100:1], labels = NULL, labcex = 0.6,
  drawlabels = TRUE, colscalelab = "free energy",
  method = "flattest", contcol = par("fg"), lty = par("lty"),
  lwd = 1, asp = NULL, axes = T, ...)

Arguments

x	fes object.
plottype	specifies whether 2D free energy surface will be plotted as image, contours or both (default "both").
colscale	specifies whether color scale will be plotted (default False).
xlim	numeric vector of length 2, giving the x coordinates range.
ylim	numeric vector of length 2, giving the y coordinates range.
zlim	numeric vector of length 2, giving the z 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'.
nlevels	number of contour levels desired if 'levels' is not supplied.
levels	numeric vector of levels at which to draw contour lines.
col	color of the free energy surface. For 1D surface it is the color of the line. For 2D it is a list of colors such as that generated by 'rainbow', 'heat.colors', 'topo.colors', 'terrain.colors' or similar functions (default=rainbow(135)[100:1]).
labels	a vector giving the labels for the contour lines. If 'NULL' then the levels are used as labels, otherwise this is coerced by 'as.character'.
labcex	'cex' for contour labeling. This is an absolute size, not a multiple of 'par("cex")'.
drawlabels	logical. Contours are labeled if 'TRUE'.
colscalelab	color scale label (default "free energy").
method	character string specifying where the labels will be located. Possible values are '"simple"', '"edge"' and '"flattest"' (the default). See the 'Details' section.
contcol	contour color.
lty	line type for the lines drawn.
lwd	contour line width.
asp	the y/x aspect ratio, see 'plot.window'.
axes	a logical value indicating whether both axes should be drawn on the plot.
...	further arguments passed to or from other methods.

Examples

tfes2d<-fes(acealanme, imax=5000)
plot(tfes2d)
tfes1d<-fes(acealanme1d)
plot(tfes1d)

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