ramachandran function

Ramachandran plot for two dihedral angles

This plotting function divides a full rotation (360 degrees) into x- and y- bins and colors them according to the number of angle pairs that are provided in the input, a so-called Ramachandran plot.

ramachandran( dihedrals,
              xBins = 150,
              yBins = 150,
              heatFun = "norm", 
              structureAreas = c(),
              plotType = "sparse",
              printLegend = FALSE,
              plotContour = FALSE,
              barePlot = FALSE,
              ... )

Arguments

• dihedrals: Matrix with angles (two columns).

• xBins: Number of x-axis bins to be plotted.

• yBins: Number of y-axis bins to be plotted.

• heatFun: Function selector for calculation of the colour, possible are either:

  • "norm" (default) for linear calculation, or
  • "log" for logarithmic calculation.

• structureAreas: List of areas, which are plotted as black lines.

• plotType: Type of plot to be used, either "sparse" (default, using function hist2d()), "comic" (own binning, use for very few datapoints) or "fancy" (3D, using function persp()).

• printLegend: Boolean, specifying whether a heat legend is to be plotted or not.

• plotContour: Boolean, specifying whether a contour should be plotted or no.

• barePlot: Boolean, indicating whether the plot is to be made without any additional information.

• ...: Additional arguments (ellipsis).

Returns

Returns a list of binned dihedral angle occurrences.

Examples

# GROMOS (see load_rmsd() for other input possibilities)
ramachandran( load_ramachandran( system.file( "extdata/ramachandran_example.txt.gz",
                                              package = "MDplot" ) ) )

Author(s)

Christian Margreitter