clusters {MDplot}

Cluster bar plot

Description

This function plots clusters over a set of trajectories as joint, coloured bar plots. The clusters are sorted beginning with the most populated one in descending order.

Usage

clusters( clusters,
          clustersNumber = NA,
          legendTitle = "trajectories",
          barePlot = FALSE,
          ... )

Arguments

clusters

Matrix with clusters: trajectories are given in row-wise, clusters in column-wise fashion as provided by load_clusters(), the associated loading function.

clustersNumber

When specified, only these first clusters are shown.

legendTitle

The title of the legend.

barePlot

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

...

Additional arguments (ellipsis).

Value

Returns a nxm-matrix with n being the number of input trajectories and m the number of different clusters. Each element in the matrix holds the number of snapshots, the respective cluster occurred in the respective trajectory.

Author(s)

Christian Margreitter

Examples

# GROMOS (see load_clusters() for other input possibilities)
clusters( load_clusters( system.file( "extdata/clusters_example.txt.gz",
                                      package = "MDplot" ) ) )