plot_cluster_trajectories-hbr-method: Method to visualize the trajectories for all identified...
In haploReconstruct: Reconstruction of Haplotype-Blocks from Time Series Data

Description Usage Arguments Details Author(s) See Also

Method to visualize the trajectories for all identified clusters in a window

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## S4 method for signature 'hbr'
plot_cluster_trajectories(object, window, ylim = c(0, 1),
  p.median = T, tp.cor = T)

`object`	object of class `hbr`
`window`	numeric specifying the number of the window, for which trajectories should be plotted.
`ylim`	numeric vector with two elements specifying the limits of the y-axis.
`p.median`	boolean specifying if the median trajectory for each cluster should be added to the plot (default: TRUE).
`tp.cor`	Boolean indicating if only the time points used for calaculating correlations `use.libs` are shown (tp.cor=T) or all time points present in the data set are shown (tp.cor=F).

The method operates on hbr objects and plots the trajectories of all clusters and replicates in the specified window. Cluster trajectories are visualized by trajectories of all markers contained in the respective clusters and median trajectories for a cluster are visualized in a different color. For each cluster it is indicated to which haplotype-block it was later assigned. NOTE: It is possible that to clusters are assigned to the identical haplotype-block. This can happen when a cluster in an overlapping window shares markers with two clusters of the "focal" window.

Susanne U. Franssen

hbr ex_dat summary.hbr plot.hbr plot_marker_trajectories map rev_map markers plot_hbr_freq inspect_window inspect_window_PCA inspect_window_avLink inspect_window_dbScan number_hbr