rmsd: Root-mean-square-deviation (RMSD) plot

In MDplot: Visualising Molecular Dynamics Analyses

Description

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

Usage

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

Arguments

rmsdData	List of (alternating) indices and RMSD values, as produced e.g. by load_rmsd().
printLegend	Boolean, which triggers plotting of the legend.
snapshotsPerTimeInt	Number, specifying how many snapshots are comprising 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.
legendPosition	Indicates 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

Returns a list of lists, where each sub-list represents a RMSD curve and contains:

minValue	The minimum value over the whole time range.
maxValue	The maximum value over the whole time range.
meanValue	The mean value calculated over the whole time range.
sd	The standard deviation calculated over the whole time range.

Author(s)

Christian Margreitter

Examples

# GROMOS (see load_rmsd() for other input possibilities)
rmsd( load_rmsd( c( system.file( "extdata/rmsd_example_1.txt.gz", package = "MDplot" ),
                    system.file( "extdata/rmsd_example_2.txt.gz", package = "MDplot" ) ) ) )

Example output

Loading required package: MASS
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: gtools
[[1]]
[[1]]$minValue
[1] 0

[[1]]$maxValue
[1] 0.30141

[[1]]$meanValue
[1] 0.2005958

[[1]]$sd
[1] 0.04307284


[[2]]
[[2]]$minValue
[1] 0

[[2]]$maxValue
[1] 0.31472

[[2]]$meanValue
[1] 0.2024374

[[2]]$sd
[1] 0.0444037

MDplot documentation built on May 2, 2019, 7:02 a.m.