rmsf function

Root-mean-square-fluctuation (RMSF) plot

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

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).

Returns

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" ) ) ) )

Author(s)

Christian Margreitter