haploReconstruct (version 0.1.2)

inspect_window_PCA,hbr-method: PCA of haplotype-block marker for a window

Description

Plots all filtered SNPs for a given window in terms of their the first two principal components of the respective time series data.

Usage

"inspect_window_PCA"(object, window)

Arguments

object

object of class hbr containing the results of reconstructed haplotype-blocks

window

number of the window, which should be inspected

Details

Performs principal component analysis (PCA) on the time series data of the filtered SNPs and the selected time points (filtered and selected through use.libs in initialize_SNP_time_series) in a given window. SNPs are shown in terms of the first two principal components and colored according to the haplotype-block they were assigned to. Black colored points were not assigned to any cluster.

See Also

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