MDplot (version 0.2)

dssp_summary: DSSP summary 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 takes hydrogen bonds into account. The default order is: "3-Helix", "4-Helix", "5-Helix", "Bend", "Beta-Bridge", "Beta-Strand", "Turn".

Usage

dssp_summary( dsspData,
              printLegend = FALSE,
              useOwnLegend = FALSE,
              motifNames = NA,
              colours = NA,
              showValues = NA,
              showResidues = NA,
              plotType = "dots",
              selectedMotifs = 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 motifs are considered to be in default order.

motifNames

Vector of names for the secondary structure motifs.

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.

selectedMotifs

A vector of names of the motifs selected for plotting.

barePlot

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

...

Additional arguments (ellipsis).

Examples

# see "extdata/dssp_summary_example.txt.gz" for format information
dssp_summary( load_dssp_summary( system.file( "extdata/dssp_summary_example.txt.gz",
                                 package = "MDplot" ) ) )