clusters_ts: Cluster timeseries plot

In MDplot: Visualising Molecular Dynamics Analyses

Description

This function plots distributions between clusters over time. In the top sub-plot, the overall distribution is given, while the timeseries is given at the bottom. The clusters are sorted beginning with the most populated one and then in descending order. Selections can be made and clusters that are not selected do also not appear in the timeseries plot (white areas).

Usage

clusters_ts( clustersDataTS,
             clustersNumber = NA,
             selectTraj = NA,
             selectTime = NA,
             timeUnit = NA,
             snapshotsPerTimeInt = 1000,
             ... )

Arguments

clustersDataTS	List of cluster information as provided by load_clusters_ts(), the associated loading function.
clustersNumber	Integer, specifying the number of clusters that is to be plotted.
selectTraj	Vector of indices of trajectories that are to be plotted (as given in the input file).
selectTime	Range of time in snapshots, which is to be plotted.
timeUnit	Abbreviation of time unit.
snapshotsPerTimeInt	Specifies, how many snapshots make up one time unit.
...	Additional arguments (ellipsis).

Value

Returns a summary (n+1)xm-matrix with n being the number of input trajectories and m the number of different clusters (which have been plotted). Each element in the matrix holds the number of snapshots, the respective cluster occured in the respective trajectory. In addition, the first line is the overall summary counted over all trajectories.

Author(s)

Christian Margreitter

Examples

# GROMOS (see load_clusters_ts() for other input possibilities)
clusters_ts( load_clusters_ts( system.file( "extdata/clusters_ts_example.txt.gz",
                               package = "MDplot" ),
                               lengths = c( 4000, 4000, 4000, 4000, 4000, 4000 ) ),
             clustersNumber = 7 )

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
            cluster1 cluster2 cluster3 cluster4 cluster5 cluster6 cluster7
overall        61.05    11.66     7.38     5.74     1.84     1.80     1.47
trajectory1    99.10     0.02     0.05     0.02     0.00     0.00     0.02
trajectory2    33.23     0.10    44.22     0.00     1.12     0.00     0.00
trajectory3    97.32     0.48     0.00     0.00     0.00     0.12     0.00
trajectory4    62.82    18.52     0.00     0.00     0.00     0.73     8.77
trajectory5    38.12     0.10     0.00    34.42     9.88     0.00     0.00
trajectory6    35.70    50.75     0.00     0.00     0.02     9.95     0.00

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