plot.fes: Free energy surface plotter

In sucurz/testing: Metadynminer reads, analyses and visualizes metadynamics HILLS files from Plumed.

Description

The function recognizes whether the free energy surface (FES) is 1D or 2D. A 1D FES is ploted as a free energy profile. A 2D FES is ploted as a heatmap (function image) and as contours.

Usage

plot.fes(inputfes, plottype = "both",
         nlevels = 10, levels = NULL, col = rainbow(135)[100:1],
         labels = NULL, labcex = 0.6, drawlabels = TRUE, contcol=par("fg"), ...)

Arguments

inputfes	The object inputfes is a free energy surface calculated by function mtdfes, mtdfes2 or read by read.fes.
plottype	type what type of plot should be drawn. Plot type choice is irelevant for 1D FES. Possible types are both plots both colored heatmap (image) and contours. It is deafault. image plots colored heatmap (image) only contour plots contours only.
nlevels	number of contour levels desired levels is not supplied.
levels	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.
col	a list of image colors such as that generated by rainbow, heat.colors, topo.colors, terrain.colors or similar functions.
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 labelling. This is an absolute size, not a multiple of par("cex").
drawlabels
method
contcol

Author(s)

Vojtech Spiwok

Examples

  data(acealanme1.3)
  myfes<-mtdfes(acealanme1.3)
  plot(myfes)

sucurz/testing documentation built on May 29, 2019, 9:51 a.m.