misc.wrappers

Under Developement

Package Description

This package includes functions to fascilitate running some popular programs used for assessing population structure, demographic modelling, and genetic/genomic and phylogenetic/genomic programs, and to summarize results in useful ways. The main functions are shown in the table below along with example input and output files. The values used for function arguments, not shown in table, also control analyses and should be set mindfully - see examples (will add soon) of function usage.

Install misc.wrappers from GitHub using devtools, remotes, or BiocManager

# with devtools:
library(devtools)
devtools::install_github("JeffWeinell/misc.wrappers")

# with remotes:
library(remotes)
remotes::install_github("JeffWeinell/misc.wrappers")

# with BiocManager:
library(BiocManager)
BiocManager::install("JeffWeinell/misc.wrappers")

Software Requirements

Some functions depend on other programs to be installed. In particular, run_fastStructure requires fastStructure to be installed, and runeems_snps_setup requires EEMS to be installed.

Download, unpack, and install EEMS

Follow the instructions here on how to download the EEMS repository, which includes several programs, including runeems_snps which you must install from source.

Download, unpack, and install fastStructure

Follow the instructions here on how to install fastStructure

(Optionally) link misc.wrappers to the programs that it depends on. If this is skipped you will need either add the location of these programs to your system path or provide the full paths as arguments when running functions.

If runeems_snps is installed on your PATH, then you can skip this step. Otherwise, use the function config_miscwrappers to tell misc.wrappers where to find runeems_snps. You only need to do this once.

library(misc.wrappers)
# Link the EEMS program 'runeems_snps'
config_miscwrappers(exe.paths="*/eems-master/runeems_snps/src/runeems_snps")

# Link python 2 (required by fastStructure) and the fastStructure program 'structure.py'.
config_miscwrappers(exe.paths=c("*/PATH/TO/python","*/fastStructure-master/structure.py"))

run_DAPC Run DAPC from SNP data in a VCF file and plot results

library(misc.wrappers)
## Example 1: 
# Define path to a VCF file that contains simulated SNP data, or, set the path to a file your own data.
vcf.path    <- file.path(system.file("extdata", package = "misc.wrappers"),"simK4.vcf.gz")
# Run DAPC analyses and save the results to files in your current directory.
run_DAPC(x=vcf.path,format="VCF",kmax=10,samplenames=NULL,reps=30,include.out=c(".pdf"))

## Example 2: Same SNP dataset as example 1, but here we also provide Lon/Lat coordinates of individuals to geographically interpolate population assignments.
# Path to VCF file
vcf.path    <- file.path(system.file("extdata", package = "misc.wrappers"),"simK4.vcf.gz")
# Path to coordinates file
coords.path <- file.path(system.file("extdata", package = "misc.wrappers"),"simK4_coords.txt")
# Running DAPC analyses
run_DAPC(x=vcf.path, format="VCF", kmax=10, coords=coords.path, samplenames=NULL, reps=30, include.out=c(".pdf"))

run_sNMF Run sNMF/LEA from SNP data in a VCF file and plot results

library(misc.wrappers)

## Example 1:
# Path to VCF with SNPs
vcf.path    <- file.path(system.file("extdata", package = "misc.wrappers"),"simK4.vcf.gz")
run_sNMF(x=vcf.path,format="VCF",kmax=10,reps=30,save.as="sNMF_simK4.pdf")

## Example 2: Same SNP dataset as example 1, but here we also provide Lon/Lat coordinates of individuals to geographically interpolate admixture coefficients.
vcf.path    <- file.path(system.file("extdata", package = "misc.wrappers"),"simK4.vcf.gz")
coords.path <- file.path(system.file("extdata", package = "misc.wrappers"),"simK4_coords.txt")
run_sNMF(x=vcf.path, format="VCF", coords=coords.path, samplenames=NULL, kmax=10, reps=30, entropy=TRUE, project="new", iter=500)

run_fastStructure Run fastStructure from SNP data in a VCF file and and plot results.

library(misc.wrappers)
## Example 1:
# Path to VCF with SNPs
vcf.path    <- file.path(system.file("extdata", package = "misc.wrappers"),"simK4.vcf.gz")
# Run fastStructure 30 times each for K=1-10
run_fastStructure(x=vcf.path,kmax=10,reps=30,save.as="fs_simK4.pdf",include.out=c(".pdf"))

## Example 2: Same SNP dataset as example 1, but here we also provide Lon/Lat coordinates of individuals to geographically interpolate admixture coefficients.
vcf.path    <- file.path(system.file("extdata", package = "misc.wrappers"), "simK4.vcf.gz")
coords.path <- file.path(system.file("extdata", package = "misc.wrappers"), "simK4_coords.txt")
run_fastStructure(x=vcf.path, coords=coords.path, kmax=10, reps=30, include.out=c(".pdf"))

runtess Run tess3r from SNP data in a VCF file and plot results

library(misc.wrappers)

# Path to VCF with SNPs
vcf.path    <- file.path(system.file("extdata", package = "misc.wrappers"), "simK4.vcf.gz")
# Path to file with longitude and latitude of sampling locality of each individual
coords.path <- file.path(system.file("extdata", package = "misc.wrappers"), "simK4_coords.txt")
# Run tess3r 30 times each for K=1-10
runtess(x=vcf.path,coords=coords.path,kmax=10,reps=30)

plot_model Create a graphical representation of a demographic model that is defined by a template (.tpl) and estimation (.est) file.

library(misc.wrappers)
example_est <- "file.path(system.file("extdata", package = "misc.wrappers"), "example.est")"
example_tpl <- "file.path(system.file("extdata", package = "misc.wrappers"), "example.tpl")"
model.obj   <- plot_model(tpl.path=example_tpl,  est.path=example_est)
pdf("example_model.pdf", width=10,height=6)
model.obj
dev.off()

Cartoon graph of the model defined by example.tpl and example.est:

create.outer. Generates a set of outer habitat coordinates that can be used for EEMS

This function takes as input a file with coordinates of samples. Example input file: coords.txt

library(misc.wrappers)
# Sample 50 points from 10-degree radius area with center located on land somewhere between -50 and 50 degrees latitude.
coords50 <- rcoords(r=10,size=50,limits=c(-180,180,-50,50))

# Using method 1 to create the outer set of points and generate a figure with points on map. Method 1 may not work well for points on continents vs. island archipelagos.
coords50_outer1 <- create.outer(coords=coords50, method=1, output.path="coords50_outer1.txt", plot.output.path="coords50_outer1.pdf")

Method 1 output: outer1.txt

# Using method 2
coords50_outer2 <- create.outer(coords=coords50, method=2, output.path="coords50_outer2.txt", plot.output.path="coords50_outer2.pdf")

Method 2 output: outer2.txt

# Using method 3
coords50_outer3 <- create.outer(coords=coords50, method=3, output.path="coords50_outer3.txt", plot.output.path="coords50_outer3.pdf")

Method 3 output: outer3.txt

runeems_snps_setup Generate input files for runeems_snps

This function takes as input two files: (1) SNPs in a VCF file and (2) a two-column text file with longitude and latitude coordinates for each individual in the VCF file. Output of this function includes all of the files and directories necessary for running EEMS (see example below), including bash scripts for running EEMS.

library(misc.wrappers)

# Path to VCF with SNPs
vcf.path    <- file.path(system.file("extdata", package = "misc.wrappers"), "simK4.vcf.gz")
# Path to file with longitude and latitude of sampling locality of each individual
coords.path <- file.path(system.file("extdata", package = "misc.wrappers"), "simK4_coords.txt")
# Where to save output
save.path   <- file.path(system.file("examples", package = "misc.wrappers"),"simK4")
# Setup environment and input files for runeems_snps
eems.setup  <- runeems_snps_setup(x=vcf.path, coords=coords.path, save.in=save.path, numMCMCIter = 100000, numBurnIter = 10000, numThinIter = 999)

Running runeems_snps_setup will create the directory specified by the argument 'save.in', and the following files and subdirectories: