MDplot (version 0.2)

rmsd: Root-mean-square-deviation plot

Description

Plot one (or more) RMSD files as produced by molecular dynamics packages.

Usage

rmsd( rmsdData,
      printLegend = TRUE,
      factor = 1000,
      timeUnit = "ns",
      rmsdUnit = "nm",
      colours = NA,
      names = NA,
      barePlot = FALSE,
      ... )

Arguments

rmsdData

List of (alterating) indices and rmsd values, as also produced by MDplot::load_rmsd() for example.

printLegend

Boolean, which triggers plotting of the legend.

factor

Number, specifying how many snapshots are within one timeUnit.

timeUnit

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

rmsdUnit

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

colours

Vector of colours used for plotting.

names

Vector of the names of the trajectories.

barePlot

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

...

Additional arguments (ellipsis).

Examples

# two curves
rmsd( load_rmsd( c( system.file( "extdata/rmsd1_example.txt.gz", package = "MDplot" ),
                    system.file( "extdata/rmsd2_example.txt.gz", package = "MDplot" ) ) ) )