plot.minima: Plot minima object

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

Plot minima object

Description

'plot.minima' plots free energy surface with minima. The free energy surface is plotted the same way as by plot.fes with additional minima labels.

Usage

## S3 method for class 'minima'
plot(x, plottype = "both", xlim = NULL, ylim = NULL,
  zlim = NULL, colscale = F, colscalelab = "free energy",
  main = NULL, sub = NULL, xlab = NULL, ylab = NULL,
  nlevels = 10, levels = NULL, col = rainbow(135)[100:1],
  labels = NULL, labcex = 0.6, drawlabels = TRUE,
  method = "flattest", textcol = "black", pch = 1, bg = "red",
  cex = 1, contcol = par("fg"), lty = par("lty"), lwd = par("lwd"),
  asp = NULL, axes = TRUE, ...)

Arguments

x	minima object.
plottype	specifies whether 2D free energy surface will be plotted as image, contours or both (default "both").
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.
colscale	specifies whether color scale will be plotted (default False).
colscalelab	color scale label (default "free energy").
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'.
method	character string specifying where the labels will be located. Possible values are '"simple"', '"edge"' and '"flattest"' (the default). See the 'Details' section.
textcol	color of minima labels.
pch	plotting 'character', i.e., symbol to use. See 'points'
bg	background (fill) color for the open plot symbols given by 'pch = 21:25'.
cex	character (or symbol) expansion: a numerical vector. This works as a multiple of 'par("cex")'.
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

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

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