plot_run_statistics: Summarize data grouped by sequencing run.

In eriqande/microhaplotopia: Tools for Working with Microhaplot Data a la the SWFSC

Description

Plot summaries of read depth per locus, reads per sample, and haplotypes per locus by sequencing run. This function can be used for raw or filtered data, but we think it would be most useful as a quick check of the filtered data before proceeding to more advanced analyses or data transformations for different programs.

Usage

plot_run_statistics(datafile, output_summary)

Arguments

datafile	dataframe of microhaplotype data. This can be filtered or unfiltered data. For example, unfiltered data such as hap_raw or filtered data such as long_genos can be used.
output_summary	summary statistic to plot. Choose one of "total_reads_per_locus", "total_reads_per_indiv" or "unique_haps_per_locus". Plotting all 3 summary statistics in a single window is uninterpretable. So look at each summary statistic separately.

eriqande/microhaplotopia documentation built on July 7, 2020, 1:16 a.m.