In sa-lee/starmie: Population Structure Model Inference and Visualisation

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "inst/vignette-supp/",
  tidy = TRUE
)

Quick Start

Construct a barplot for your STRUCTURE/ADMIXTURE output using starmie in a few lines of code!

# install.packages("starmie")
library(starmie)
str_output <- system.file("extdata/microsat_testfiles/",  "locprior_K5.out_f", package = "starmie")
k5_data <- loadStructure(str_output)
k5_data
plotBar(k5_data, facet = FALSE)

intro_rmd <- 'vignettes/using-starmie.Rmd'

raw_rmd <- readLines(intro_rmd)

# remove yaml 
yaml_lines <- grep("---", raw_rmd)

# remove appendix (session info)
appendix <- grep("Appendix", raw_rmd)

compressed_rmd <- raw_rmd[c(-seq(yaml_lines[1], yaml_lines[2], by = 1), 
                            -seq(appendix, length(raw_rmd)))]
writeLines(compressed_rmd, "child.Rmd")

Installation

starmie is available as an R package on CRAN

install.packages("starmie")

The development version of starmie can be installed with devtools

install.packages("devtools")

devtools::install_github("sa-lee/starmie")

If you would like to also build the vignette with your installation run:

devtools::install_github("sa-lee/starmie", build_vignettes = TRUE)

if (file.exists("child.Rmd")) {
  file.remove("child.Rmd")
}

sa-lee/starmie documentation built on May 28, 2019, 11 a.m.