haploReconstruct (version 0.1.2)

plot_marker_trajectories,hbr-method: Method to visualize the trajectories for all markers in a haplotype-block

Description

Method to visualize the trajectories for all markers in a haplotype-block

Usage

"plot_marker_trajectories"(object, hbr_id, ylim = c(0, 1), loc.col = T, tp.cor = T)

Arguments

object

object of class hbr

hbr_id

the id of the haplotype-block, for which the marker trajectories should be plotted.

ylim

numeric vector with two elements specifying the limits of the y-axis.

loc.col

boolean indicating if trajectories should be coloured ranging from red over blue to yellow according to their location on the chromosome (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 markers in a haplotype-block in all replicates. Note: As blocks can span a wide range along the genome, it is not expected that trajectories within a block stay very similar. Changing location along the genome can be indicated with loc.col=T.

See Also

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