EvalAdmix - Revision history

Albrecht at 17:57, 4 March 2024

2024-03-04T17:57:07Z

← Older revision		Revision as of 19:57, 4 March 2024
Line 95:		Line 95:
	Download the input file containing genotypes in binary plink format		Download the input file containing genotypes in binary plink format
	<pre>		<pre>
	wget ~~http~~://~~pontus.~~popgen.dk/albrecht/open/admixTjeck/plink/admixTjeck2.bed		wget https://popgen.dk/albrecht/open/admixTjeck/plink/admixTjeck2.bed
	wget ~~http~~://~~pontus.~~popgen.dk/albrecht/open/admixTjeck/plink/admixTjeck2.bim		wget https://popgen.dk/albrecht/open/admixTjeck/plink/admixTjeck2.bim
	wget ~~http~~://~~pontus.~~popgen.dk/albrecht/open/admixTjeck/plink/admixTjeck2.fam		wget https://popgen.dk/albrecht/open/admixTjeck/plink/admixTjeck2.fam
	</pre>		</pre>

2024-01-11T10:09:38Z

2022-12-27T09:27:51Z

Genotype data

← Older revision		Revision as of 11:27, 27 December 2022
Line 116:		Line 116:
	::Admixture proportions file admixTjeck2.3.Q (-qname admixTjeck2.3.Q).		::Admixture proportions file admixTjeck2.3.Q (-qname admixTjeck2.3.Q).
	::Computer cores = 20 (-P 20).		::Computer cores = 20 (-P 20).


	Plot results in R		Plot results in R
			[[File:evalAdmixK3.Q.png\|thumb\|frame\|admixture proportions]]
			[[File:evalAdmixK3.cor.png\|thumb\|frame\|evalAdmix correlations]]
	<pre>		<pre>
	source("visFuns.R")		source("visFuns.R")
Line 141:		Line 144:

	</pre>		</pre>
	~~[[File:evalAdmixK3.Q.png\|thumb\|frame\|admixture proportions]]~~
	~~[[File:evalAdmixK3.cor.png\|thumb\|frame\|evalAdmix correlations]]~~

	=== Low depth sequencing data ===		=== Low depth sequencing data ===

2022-12-27T09:25:20Z

Genotype data

← Older revision		Revision as of 11:25, 27 December 2022
Line 141:		Line 141:

	</pre>		</pre>
			[[File:evalAdmixK3.Q.png\|thumb\|frame\|admixture proportions]]
			[[File:evalAdmixK3.cor.png\|thumb\|frame\|evalAdmix correlations]]

	=== Low depth sequencing data ===		=== Low depth sequencing data ===

2022-12-27T09:16:14Z

Run command example

← Older revision		Revision as of 11:16, 27 December 2022
Line 129:		Line 129:
	# order according to population and plot the ADMIXTURE reults		# order according to population and plot the ADMIXTURE reults
	ord<-orderInds(pop = as.vector(pop[,2]), q = q)		ord<-orderInds(pop = as.vector(pop[,2]), q = q)
	barplot(t(q)[,ord~~],col~~=~~2:10,space=0,border=NA,xlab="Individuals",ylab="Demo2 Admixture proportions for K=3")~~
	~~text(sort(tapply(1:nrow(pop),pop[~~ord,~~2],mean)),-0.05,unique(~~pop~~[ord,2]),xpd=T)~~		#make barplot
	~~abline(v~~=~~cumsum(sapply(unique(~~pop[~~ord~~,2])~~,function(x){sum(pop[ord,2]==x)})),col=1,lwd=1.2)~~		plotAdmix(q,ord=ord,pop=pop[,2])

2022-12-27T09:13:09Z

Genotype data

← Older revision		Revision as of 11:13, 27 December 2022
Line 123:		Line 123:
	# read population labels and estimated admixture proportions		# read population labels and estimated admixture proportions
	pop<-read.table("admixTjeck2.fam")		pop<-read.table("admixTjeck2.fam")
	q<-read.table("admixTjeck2.3.Q")		q<-read.table("admixTjeck2.3.Q",stringsAsFactors=T)

			palette(c("#A6CEE3","#1F78B4","#B2DF8A","#33A02C","#FB9A99","#E31A1C","#FDBF6F","#FF7F00","#CAB2D6","#6A3D9A","#FFFF99","#B15928","#1B9E77","#999999"))

	# order according to population and plot the ADMIXTURE reults		# order according to population and plot the ADMIXTURE reults

2022-12-27T09:02:57Z

Genotype data

← Older revision		Revision as of 11:02, 27 December 2022
Line 105:		Line 105:

	::Genotypes file prefix admixTjeck2.bed		::Genotypes file prefix admixTjeck2.bed
	::Ancestral Populations K = 3		::Number of Ancestral Populations K = 3
			::Number of CPU threads = 20

2022-12-27T09:02:24Z

Genotype data

← Older revision		Revision as of 11:02, 27 December 2022
Line 102:		Line 102:
	Run ADMIXTURE [http://software.genetics.ucla.edu/admixture/] to obtain admixture proprotions		Run ADMIXTURE [http://software.genetics.ucla.edu/admixture/] to obtain admixture proprotions

	<pre>admixture admixTjeck2.bed 3</pre>		<pre>admixture admixTjeck2.bed 3 -j20</pre>

	::Genotypes file prefix admixTjeck2.bed		::Genotypes file prefix admixTjeck2.bed

2022-10-06T09:37:04Z

Low depth sequencing data

← Older revision		Revision as of 11:37, 6 October 2022
Line 173:		Line 173:
	ord<-orderInds(pop = as.vector(pop[,1]), q = q)		ord<-orderInds(pop = as.vector(pop[,1]), q = q)
	barplot(t(q)[,ord],col=2:10,space=0,border=NA,xlab="Individuals",ylab="Demo2 Admixture proportions for K=3")		barplot(t(q)[,ord],col=2:10,space=0,border=NA,xlab="Individuals",ylab="Demo2 Admixture proportions for K=3")
	text(tapply(1:nrow(pop),pop[ord,1],mean),-0.05,unique(pop[ord,1]),xpd=T)		text(sort(tapply(1:nrow(pop),pop[ord,1],mean)),-0.05,unique(pop[ord,1]),xpd=T)
	abline(v=cumsum(sapply(unique(pop[ord,1]),function(x){sum(pop[ord,1]==x)})),col=1,lwd=1.2)		abline(v=cumsum(sapply(unique(pop[ord,1]),function(x){sum(pop[ord,1]==x)})),col=1,lwd=1.2)

2022-10-06T09:36:50Z

Genotype data

← Older revision		Revision as of 11:36, 6 October 2022
Line 128:		Line 128:
	ord<-orderInds(pop = as.vector(pop[,2]), q = q)		ord<-orderInds(pop = as.vector(pop[,2]), q = q)
	barplot(t(q)[,ord],col=2:10,space=0,border=NA,xlab="Individuals",ylab="Demo2 Admixture proportions for K=3")		barplot(t(q)[,ord],col=2:10,space=0,border=NA,xlab="Individuals",ylab="Demo2 Admixture proportions for K=3")
	text(tapply(1:nrow(pop),pop[ord,2],mean),-0.05,unique(pop[ord,2]),xpd=T)		text(sort(tapply(1:nrow(pop),pop[ord,2],mean)),-0.05,unique(pop[ord,2]),xpd=T)
	abline(v=cumsum(sapply(unique(pop[ord,2]),function(x){sum(pop[ord,2]==x)})),col=1,lwd=1.2)		abline(v=cumsum(sapply(unique(pop[ord,2]),function(x){sum(pop[ord,2]==x)})),col=1,lwd=1.2)