MDplot (version 0.3.1)

hbond_ts: Plot hydrogen bond timeseries

Description

Timeseries plot of hydrogen bonds (various selections possible). In addition to the timeseries file, the summary file is also necessary.

Usage

hbond_ts( timeseries, summary, acceptorRange = NA, donorRange = NA, plotOccurences = FALSE, scalingFactorPlot = NA, printNames = FALSE, namesToSingle = FALSE, printAtoms = FALSE, timeUnit = NA, snapshotsPerTimeInt = 1000, timeRange = NA, hbondIndices = NA, barePlot = FALSE, ... )

Arguments

timeseries

Table, containing the timeseries information (e.g. produced by load_hbond_ts()).

summary

Table, containing the summary information (e.g. produced by load_hbond()).

acceptorRange

Vector of acceptor resdiues, which are to be plotted.

donorRange

Vector of donor residues, which are to be plotted.

plotOccurences

Specifies, whether the overall summary should also be plotted in a subplot on the right hand side.

scalingFactorPlot

To manually set the scaling factor (if necessary).

printNames

Enables human readable names rather than the hbond identifiers.

namesToSingle

If printNames is TRUE, this flags enables one letter codes.

printAtoms

Enables atom names in hydrogen bond identification on the y-axis.

timeUnit

Specifies the time unit on the x-axis.

snapshotsPerTimeInt

Specifies, how many snapshots make up one time unit (see above).

timeRange

Selects a certain time range specified by a vector.

hbondIndices

List, containing vectors to select hbonds by their identifiers.

barePlot

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

...

Additional arguments (ellipsis).

Examples

# see "extdata/hbond_example.txt.gz" and "extdata/hbond_ts_example.txt.gz" for format information
hbond_ts( load_hbond_ts( system.file( "extdata/hbond_ts_example.txt.gz",
                                      package = "MDplot" ) ),
          load_hbond( system.file( "extdata/hbond_example.txt.gz",
                                   package = "MDplot" ) ) )