MDplot (version 1.0.1)

rmsf: Root-mean-square-fluctuation (RMSF) plot

Description

Plot (multiple) RMSF file(s) as produced by molecular dynamics packages.

Usage

rmsf( rmsfData,
      printLegend = TRUE,
      rmsfUnit = "nm",
      colours = NA,
      residuewise = FALSE,
      atomsPerResidue = NA,
      names = NA,
      rangeAtoms = NA,
      legendPosition = "topright",
      barePlot = FALSE,
      ... )

Arguments

rmsfData

List of (alternating) indices and RMSF values, as produced e.g. by load_rmsf().

printLegend

Boolean, which triggers plotting of the legend.

rmsfUnit

Specifies, which unit the y-axis is given in.

colours

Vector of colours used for plotting.

residuewise

Boolean, specifying whether atoms or residues are plotted on the x-axis.

atomsPerResidue

If residuewise is TRUE, this parameter can be used to specify the number of atoms per residue for plotting.

names

Vector of the names of the trajectories.

rangeAtoms

Range of atoms to be plotted.

legendPosition

Indicate position of legend: either "bottomright", "bottomleft", "topleft" or "topright".

barePlot

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

...

Additional arguments (ellipsis).

Value

A list of vectors, alternately holding atom indices and their respective values.

Examples

# GROMOS (see load_rmsf() for other input possibilities)
rmsf( load_rmsf( c( system.file( "extdata/rmsf_example_1.txt.gz", package = "MDplot" ),
                    system.file( "extdata/rmsf_example_2.txt.gz", package = "MDplot" ) ) ) )