ramachandran {MDplot}

Ramachandran plot for two dihedral angles

Description

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.

Usage

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).

Value

Returns a list of binned dihedral angle occurrences.

Author(s)

Christian Margreitter

Examples

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