plot_hbr_freq-hbr-method: Plots frequencies of a reconstructed haplotype-block along...
In haploReconstruct: Reconstruction of Haplotype-Blocks from Time Series Data

Description Usage Arguments Details Author(s) See Also

Plots frequencies of a reconstructed haplotype-block along the chromosome

## S4 method for signature 'hbr'
plot_hbr_freq(object, hbr_id = 1, replicate, timepoint,
  window = 1, cols = NULL, add = F, sumstat = "mean", cex = 0.7,
  xlab = "Genomic position [Mb]", ylab = "Marker frequency", xlim = NULL,
  ylim = c(0, 1), pch = 20, lwd = 2)

`object`	object of class `hbr` containing the results of reconstructed haplotype-blocks
`hbr_id`	id (integer) of the haplotype-block to be plotted
`replicate`	numeric vector of integers specifying the replicates for which results should be plotted
`timepoint`	numeric vector of time points for which the results shouls be plotted
`window`	window size over which frequencies are averaged (results are plotted for windows overlapping by windows/2)
`cols`	vector of colors with the length of the specified libraries
`add`	logical specifying if a new plot should be created or haplotype-block frequencies are added to an existing plot.
`sumstat`	Summary statistics used for the y-values in a window. Either specify "mean" (the default) or "median".
`cex`	scaling of the point size in the output plot
`xlab`	x-label in the output plot
`ylab`	y-label in the output plot
`xlim`	vector of the limits on the x-axis in the output plot
`ylim`	vector of the limits on the y-axis in the output plot
`pch`	option to specify symbols to use when plotting points in the output plot
`lwd`	line width in the output plot

The plotting method operates on hbr objects and returns a plot containing frequencies of a respective haplotype-block along the chromosome for specified time points and replicates.

Susanne U. Franssen

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