`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).
# S3 method for 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, ...)fes object.
specifies whether 2D free energy surface will be plotted as image, contours or both (default "both").
specifies whether color scale will be plotted (default False).
numeric vector of length 2, giving the x coordinates range.
numeric vector of length 2, giving the y coordinates range.
numeric vector of length 2, giving the z coordinates range.
an overall title for the plot: see 'title'.
a sub title for the plot: see 'title'.
a title for the x axis: see 'title'.
a title for the y axis: see 'title'.
number of contour levels desired if 'levels' is not supplied.
numeric vector of levels at which to draw contour lines.
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]).
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'.
'cex' for contour labeling. This is an absolute size, not a multiple of 'par("cex")'.
logical. Contours are labeled if 'TRUE'.
color scale label (default "free energy").
character string specifying where the labels will be located. Possible values are '"simple"', '"edge"' and '"flattest"' (the default). See the 'Details' section.
contour color.
line type for the lines drawn.
contour line width.
the y/x aspect ratio, see 'plot.window'.
a logical value indicating whether both axes should be drawn on the plot.
further arguments passed to or from other methods.
# NOT RUN {
tfes2d<-fes(acealanme, imax=5000)
plot(tfes2d)
tfes1d<-fes(acealanme1d)
plot(tfes1d)
# }
Run the code above in your browser using DataLab