MDplot (version 1.0.1)

dssp: DSSP plot for secondary structure elements (proteins)

Description

Plots summary plot for secondary structure motifs based on the output of the widely used classification program DSSP, which uses hydrogen bonds for classification. The default order is: "3-Helix", "4-Helix", "5-Helix", "Bend", "Beta-Bridge", "Beta-Strand", "Turn" (depending on the input, not all types might be included).

Usage

dssp( dsspData,
      printLegend = FALSE,
      useOwnLegend = FALSE,
      elementNames = NA,
      colours = NA,
      showValues = NA,
      showResidues = NA,
      plotType = "dots",
      selectedElements = NA,
      barePlot = FALSE,
      ... )

Arguments

dsspData

Table containing the information on the secondary structure motifs.

printLegend

If TRUE, a legend is printed on the right hand side of the plot.

useOwnLegend

If FALSE, the names of the secondary structure elements are considered to be in default order.

elementNames

Vector of names for the secondary structure elements.

colours

A vector of colours, that can be specified to replace the default ones.

showValues

A vector of boundaries for the values (two elements).

showResidues

A vector of boundaries for the residues (two elements).

plotType

Either "dots", "curves" or "bars".

selectedElements

A vector of names of the elements selected for plotting.

barePlot

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

...

Additional arguments (ellipsis).

Value

Returns matrix, where the first column is the residue-number and the remaining ones denote secondary structure classes. Residues are given row-wise and values range from 0 to 100 percent.

Examples

# GROMOS (see load_dssp() for other input possibilities)
dssp( load_dssp( system.file( "extdata/dssp_example.txt.gz",
                 package = "MDplot" ) ) )