Plot minima object — plot.minima • metadynminer

`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.

# S3 method for 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)