haploReconstruct (version 0.1.2)

plot_cluster_trajectories,hbr-method: Method to visualize the trajectories for all identified clusters in a window

Description

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

Usage

"plot_cluster_trajectories"(object, window, ylim = c(0, 1), p.median = T, tp.cor = T)

Arguments

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).

Details

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.

See Also

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