Visualize the effect of varying a stacks parameter on the number of polymorphic loci retained

This function takes the list of dataframes output by optimize_m(), optimize_M(), or optimize_n() as input. The function then uses ggplot2 to visualize the effect of the given stacks on the number of polymorphic loci retained, reporting which value is optimal.

vis_loci(output = NULL, stacks_param = NULL)

Arguments

output	A list containing 5 dataframes generated by optimize_m()
stacks_param	A character string indicating the stacks parameter iterated over

Value

A plot showing the number of polymorphic loci retained at each given parameter value

Examples

vis_loci(output =
readRDS(system.file("extdata","optimize.m.output.RDS",package="RADstackshelpR",mustWork=TRUE)),
         stacks_param = "m")
#> Visualize how different values of m affect number of polymorphic loci retained.
#> Density plot shows the distribution of the number of loci retained in each sample,
#> while the asterisk denotes the total number of loci retained at an 80% completeness cutoff. The optimal value is denoted by red color. 
#> Picking joint bandwidth of 8.81