DrK-Lo

We have this list of IDs, and want to get the final column (right before the ".CEL" from the ID).

> s
[1] "A8_CviMVP_PlDNA_5__SG_1240__5c86242a_253268_H1.CEL"  "A9_CviMVP_PlDNA_5__SG_1659__12a25bac_253268_A2.CEL"  "A9_CviMVP_PlDNA_5__SG_1659__12a25bac_253268_A10.CEL"


This function splits the string by the "_". When doing so, the 11th value listed is the column we want and outputs eg. "H1.CEL"
Then we want to get rid of the ".CEL", so we substitute the ".CEL" with a ""
```
getstring <- function(x){a<-strsplit(x,"_");sub(".CEL","",a[[1]][11],)}

DrK-Lo

 #pl_vcf is read in with VCFR package
 ext_vcfgt_num2 <- extract.gt(pl_vcf, as.numeric = FALSE) # extract the genotype matrix from the vcf fil
  str(ext_vcfgt_num2)
  # “0/0” --> 0
  # “0/1" or “1/0” --> 1
  # “1/1" is --> 2
  FirstAllele<- matrix(as.numeric(substring(ext_vcfgt_num2,1,1)), ncol=ncol(ext_vcfgt_num2)) #first character is first allele
  SecondAllele<- matrix(as.numeric(substring(ext_vcfgt_num2,3,3)), ncol=ncol(ext_vcfgt_num2)) #third character is second allele
  Genotype <- FirstAllele + SecondAllele
  str(Genotype)

DrK-Lo

#The genotype matrix has individuals in rows and mutations #in columns, with a 0,1, or 2 entered for the number of #alternate alleles in the diploid

# Let’s create a matrix with 5 individuals, 10 SNPS, and some missing data:
set.seed(345)
GEN = matrix(sample(0:2, 50, replace=TRUE), nrow=5, ncol=10)
GEN[5,1] <- NA
GEN

# Function to calculate the allele frequency of a column
af <- function(i, gen){

DrK-Lo

ggtheme <- theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), panel.border=element_blank(), axis.line = element_line(colour="grey30"), axis.title = element_text(colour="grey20"), axis.text = (element_text(colour="grey30")), legend.title = element_text(colour="grey20"), legend.text = element_text(colour="grey30"))

to use it, just use:

ggplot(data) + geom_point(aes(x=x, y=y)) + ggtheme

DrK-Lo

par(xpd=NA, oma=c(4,0,0,0), mar=c(2,4,0,0),mfrow=c(1,1))  
plot(1,1, xlim=c(-1,1), ylim=c(0,1))
# This is for a plot with x-axis from -1 to 1 and y axis from 0 to 1. It plots a legend in the bottom margin
legend(-1,-0.25,  legend=c("high sal.", "low sal."), bty="n", adj=0, fill=c("grey", NA), horiz=TRUE)

DrK-Lo

packages_needed <- c("raster", "FNN", "RColorBrewer", "colorRamps", "adehabitatLT",
                     "data.table", "tidyverse", "fields", "ggplot2", "hexbin",
                     "rgdal", "tmap", "gstat", "sp", "maptools", "sf", "fasterize",
                     "fansi", "raster", "tmap", "gstat", "ContourFunctions","ash"
                     )

for (i in 1:length(packages_needed)){
  if(!(packages_needed[i] %in% installed.packages())){install.packages(packages_needed[i])}
}