plot.fes {metadynminer} | R Documentation

## 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)

[Package metadynminer version 0.1.6 Index]