# Project code ## Getting to our puma folder ```cd /home/ecl243-07``` ```cd puma``` ## downloading admixture ```wget http://dalexander.github.io/admixture/binaries/admixture_linux-1.3.0.tar.gz``` ## untar ```tar -zxvf admixture_linux-1.3.0.tar.gz``` ## Running ADMIXTURE ` Run ADXTURE with the .bed file ``` #!/bin/bash #SBATCH --job-name=admixture #SBATCH --nodes 1 #SBATCH --ntasks 1 #SBATCH --time 12:00:00 #SBATCH --mem=2GB #SBATCH -o puma_admix_K2.out #SBATCH --partition=ecl243 #SBATCH --error admix_errors.err #SBATCH --mail-type=ALL #SBATCH --mail-user=mgserrano@ucdavis.edu /home/ecl243-07/bin/dist/admixture_linux-1.3.0/admixture --cv /home/ecl243-07/puma/pumabed.bed 2 ``` ## converting .ped to .bed ``` module load plink plink --file /home/ecl243-07/puma/pumaco2.ped --out /home/ecl243-07/puma/pumabed --make-bed --dog ``` ## Download data from Farm sftp -P 2022 user@farm.cse.ucdavis.edu get /path/to/file sftp -P 2022 ecl243-07@farm.cse.ucdavis.edu get /home/ecl243-07/puma/pumabed.2.Q ## Making Graph ``` dat <-read.csv ("pumaQdata.csv", header=TRUE) library (ggplot2) q <- ggplot(dat, aes(fill = Ancestry, y = Percentage, x = Population)) + geom_bar(position = "stack", stat = "identity") + scale_fill_manual(values = c("mediumseagreen", "maroon4", "red", "orange2", "royalblue4", "honeydew4")) q + theme(axis.text.x = element_text(angle = 90, hjust = 1)) p <- q + theme_classic() p ``` ### Changes made from Lauren's ``` dat <-read.csv ("pumaQdata.csv", header=TRUE) library (ggplot2) q <- ggplot(dat, aes(fill = "Ancestry", x = "Percentage", y = "Population")) + geom_bar(position = "stack", stat = "identity") + scale_fill_manual(values = c("mediumseagreen", "maroon4", "red", "orange2", "royalblue4", "honeydew4")) q + theme(axis.text.x = element_text(angle = 90, hjust = 1)) p <- q + theme_classic() p ``` ### This one worked for me!! ### ``` tbl <- read.csv("pumaQdata.csv") barplot(t(as.matrix(tbl)), col=rainbow(3), xlab="Individual #", ylab="Ancestry", border=NA) ``` The output was saved as a pdf file and edited with adobe illustrator.