inst/doc/Week1_vignette.R

In hhwagner1/LandGenCourse: Interface for course "Landscape Genetic Data Analysis with R"

## ----message=FALSE, warning=TRUE---------------------------------------------------------------------
if(!require("adegenet")) install.packages("adegenet")
if(!requireNamespace("popgraph", quietly = TRUE))
{
  install.packages(c("RgoogleMaps", "geosphere", "proto", "sampling", 
                      "seqinr", "spacetime", "spdep"), dependencies=TRUE)
  remotes::install_github("dyerlab/popgraph")
}
if(!requireNamespace("gstudio", quietly = TRUE)) remotes::install_github("dyerlab/gstudio")


## ----message=FALSE, warning=TRUE---------------------------------------------------------------------
library(adegenet)
library(gstudio)
library(LandGenCourse)
library(tibble)
library(here)
library(vcfR)
library(pinfsc50)
library(utils)


## ----------------------------------------------------------------------------------------------------
data(ralu.loci)


## ----------------------------------------------------------------------------------------------------
if(!dir.exists(paste0(here(),"/downloads"))) dir.create(paste0(here(),"/downloads"))
file.copy(system.file("extdata", "ralu.loci.csv", package = "LandGenCourse"),
          paste0(here(), "/downloads/ralu.loci.csv"), overwrite=FALSE)


## ----message=FALSE, include=FALSE, out.width=5-------------------------------------------------------
fig.source <- system.file("extdata", "ExcelTable.png", package = "LandGenCourse")
fig.path <- paste0(here::here(), "/downloads/ExcelTable.png")
invisible(file.copy(from=fig.source, to=fig.path)) 


## ----echo=FALSE, results='asis'----------------------------------------------------------------------
cat(paste0("![](", fig.path, "){width=80%}"))


## ----------------------------------------------------------------------------------------------------
Frogs <- read.csv(paste0(here(), "/downloads/ralu.loci.csv"), header=TRUE)
as_tibble(Frogs)


## ----------------------------------------------------------------------------------------------------
Frogs <- data.frame(FrogID = paste(substr(Frogs$Pop, 1, 3), row.names(Frogs), sep="."), Frogs)
as_tibble(Frogs)


## ----------------------------------------------------------------------------------------------------
here() 
paste0(here(),"/output")


## ----------------------------------------------------------------------------------------------------
if(!dir.exists(paste0(here(),"/output"))) dir.create(paste0(here(),"/output"))


## ----------------------------------------------------------------------------------------------------
write.csv(ralu.loci, paste0(here(),"/output/ralu.loci.csv"), 
          quote=FALSE, row.names=FALSE)


## ----------------------------------------------------------------------------------------------------
ralu.loci.2 <- read.csv(paste0(here(),"/output/ralu.loci.csv"), header=TRUE)


## ----------------------------------------------------------------------------------------------------
?df2genind


## ----------------------------------------------------------------------------------------------------
Frogs.genind <- df2genind(X=Frogs[,c(4:11)], sep=":", ncode=NULL, ind.names= Frogs$FrogID, loc.names=NULL, pop=Frogs$Pop, NA.char="NA", ploidy=2, type="codom", strata=NULL, hierarchy=NULL)


## ----------------------------------------------------------------------------------------------------
Frogs.genind


## ----------------------------------------------------------------------------------------------------
summary(Frogs.genind)


## ----------------------------------------------------------------------------------------------------
as_tibble(Frogs.genind@tab)


## ----------------------------------------------------------------------------------------------------
Frogs.genind@loc.n.all


## ----------------------------------------------------------------------------------------------------
Frogs.genind@loc.fac


## ----------------------------------------------------------------------------------------------------
Frogs.genind@all.names


## ----------------------------------------------------------------------------------------------------
?read_population


## ----------------------------------------------------------------------------------------------------
Frogs.gstudio <- read_population(path=system.file("extdata", "ralu.loci.csv", 
                                                  package = "LandGenCourse"), 
                   type="separated", locus.columns=c(3:10), 
                   phased=FALSE, sep=",", header=TRUE)


## ----------------------------------------------------------------------------------------------------
str(Frogs.gstudio)


## ----------------------------------------------------------------------------------------------------
Frogs.gstudio <- data.frame(FrogID=Frogs$FrogID, Frogs.gstudio) 
head(Frogs.gstudio)


## ----------------------------------------------------------------------------------------------------
Frogs.genind2 <- adegenet::df2genind(X=Frogs.gstudio[,c(4:11)], sep=":", ncode=NULL,   
                          ind.names=Frogs.gstudio$FrogID, loc.names=NULL, 
                          pop=Frogs.gstudio$Pop, NA.char="", ploidy=2, 
                          type="codom", strata=NULL, hierarchy=NULL)
Frogs.genind2


## ----------------------------------------------------------------------------------------------------
infile <- system.file("extdata", "WWP_SNP_genotypes.txt", package = "LandGenCourse")
Trees <- read.table(infile, header = TRUE, sep = "\t")
Trees[1:6, 1:6]


## ----------------------------------------------------------------------------------------------------
names(Trees) <- unlist(lapply(names(Trees), function(x) strsplit(x, "[.]")[[1]][1]))


## ----------------------------------------------------------------------------------------------------
Trees.genind <- adegenet::df2genind(X=Trees[,-c(1:2)], sep="", ncode=1,   
                          ind.names=Trees$family, loc.names=NULL, 
                          pop=Trees$population, NA.char="NA", ploidy=2, 
                          type="codom", strata=NULL, hierarchy=NULL)
Trees.genind


## ----------------------------------------------------------------------------------------------------
vcf_file <- system.file("extdata", "pinf_sc50.vcf.gz", package = "pinfsc50")
vcf <- read.vcfR( vcf_file, verbose = FALSE )


## ----------------------------------------------------------------------------------------------------
SNP_genind <- vcfR2genind(vcf)
SNP_genind


## ----------------------------------------------------------------------------------------------------
SNP_genlight <- vcfR2genlight(vcf)
SNP_genlight


## ----------------------------------------------------------------------------------------------------
file.copy(system.file("extdata", "pulsatilla_genotypes.csv", package = "LandGenCourse"),
          paste0(here(), "/downloads/pulsatilla_genotypes.csv"), overwrite=FALSE)


## ----message=FALSE, warning=TRUE, include=FALSE------------------------------------------------------
# Note: this line of code detaches all packages that were loaded. This is necessary only for technical reasons of building the R package.
LandGenCourse::detachAllPackages()