vis_loci: Visualize the effect of varying a stacks parameter on the...

In DevonDeRaad/RADstackshelpR: Optimize the De Novo Stacks Pipeline via R

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

Description

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.

Usage

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")

DevonDeRaad/RADstackshelpR documentation built on June 18, 2022, 4:08 p.m.