not-package/simulations/02_makecharts_1.R

In eriqande/SNPcontam: Detecting contaminated samples from SNP genotypes

# short script to produce charts from thethe MCMC simulation

# this script should be run from the directory that includes the directories "simulations", "supplements", 
# and "manuscript"
if(!all(file.exists("simulations", "manuscript", "supplements")))  {
  stop("You must run 01_simulation_1.R in directory that includes: \"simulations\", \"manuscript\", \"supplements\"")
}

load("simulations/out_list_01.rda")
source("simulations/simulation_functions.R")

library(ggplot2)
library(grid)
library(gridExtra)


message("     making manuscript/images/rho_and_allele.pdf")
#### Produce the rho boxplots
rho_plot <- MCMC_rhoplot(rho_df = out_list_01$rho, rhovals = out_list_01$rhovals)

#### Produce the allele figure
allele_plot <- MCMC_alleleplot(allele_df = out_list_01$allele, rho = .2, loci = 20)

#### Combine and save the allele and rho figures
pdf("manuscript/images/rho_and_allele.pdf",width=5,height=6)
grid.arrange(rho_plot,allele_plot,ncol=1)
dev.off()

#### Make the Histograms of the z-values
message("     making supplements/images/histogram_*.pdf")
# the code saves the graphs into 5 separate files
# width and height denote the dementions of the pdf files
MCMC_hist(z_df = out_list_01$z, types = out_list_01$types, width = 11, height = 6, outpath = "supplements/images")