ClusterInvasionSFS

• All sites
  • simulations
  • R-graphics
  • results
• separate cluster and non-cluster insertions
  • simulations
  • R-graphics
  • results

All sites

simulations

java -jar invade.jar cluster --genome "mb:1,1,1,1" --rr "cm_mb:3,3,3,3" --cluster "kb:30,30,30,30" --u 0.05 --N 1000 --gen 10000 --basepop "seg:300" --rep 1 --silent --steps 100 --sfs-file sfs.txt

R-graphics

library(ggplot2)
library(RColorBrewer)
library(plyr)
theme_set(theme_bw())

t<-read.table("/Users/robertkofler/dev/invade/out/artifacts/invade_jar/sfs.txt")
names(t)<-c("replicate","generation","id","siteclass","fraction")

# Filter: all and some generations of interest
all<-subset(t,id=="all" & replicate==1)
all<-subset(all, generation==0 |generation==100 |generation==400 |generation ==1000| generation ==2000|generation ==4000|generation ==6000)
all$generation<-as.factor(all$generation)


# factor
g<-ggplot(all,aes(x=siteclass,y=fraction))+geom_bar(stat="identity")+facet_grid(generation ~ .)+
xlab("Site frequency class (%)")

pdf(file="/Users/robertkofler/dev/invade/out/artifacts/invade_jar/invasion-sfs.pdf",width=6,height=8)
plot(g)
dev.off()

results

separate cluster and non-cluster insertions

simulations

java -jar invade.jar cluster --genome "mb:1,1,1,1" --rr "cm_mb:3,3,3,3" --cluster "kb:30,30,30,30" --u 0.05 --N 1000 --gen 10000 --basepop "seg:300" --rep 1 --silent --steps 100 --sfs-file sfs.txt

R-graphics

library(ggplot2)
library(RColorBrewer)
library(plyr)
theme_set(theme_bw())

t<-read.table("/Users/robertkofler/dev/invade/out/artifacts/invade_jar/sfs.txt")
names(t)<-c("replicate","generation","id","siteclass","fraction")

# Filter: all and some generations of interest
all<-subset(t,id=="cluster" | id=="noncluster")
all<-subset(all, generation==0 |generation==100 |generation==400 |generation ==1000| generation ==2000|generation ==4000|generation ==6000)
all$generation<-as.factor(all$generation)

# order factor with noncluster comeing first
all$id <- factor(all$id, levels=c("noncluster", "cluster"))


# factor
g<-ggplot(all,aes(x=siteclass,y=fraction))+geom_bar(stat="identity")+facet_grid(generation ~ id)+
xlab("Site frequency class (%)")

pdf(file="/Users/robertkofler/dev/invade/out/artifacts/invade_jar/invasion-sfsclunoclue.pdf",width=6,height=6)
plot(g)
dev.off()

results