Recent changes to Invasion

Invasion modified by Robert Kofler

Robert Kofler — Wed, 06 Feb 2019 13:46:58 -0000

Invasion modified by Robert Kofler

Robert Kofler — Wed, 06 Feb 2019 13:46:28 -0000

--- v11
+++ v12
@@ -15,9 +15,24 @@
 We used a transposition rate of u=0.1 a population size of N=1000, a starting number of TEs of c0=10 and simulated the invasion for 100 generations. 
 A chromosome of size 1Mb and no piRNA clusters were simulated. We used 500 replicates.

+Which yields the following results:
+[[img src=obs-exp-inv.png]]
+
+* bold line: expectations based on the equation shown above
+* grey lines: observed invasions for 500 replicates
+
+
+## Conclusion
+Invade accurately reproduces the expected exponential increase of TE copy numbers in a population (no piRNA clusters). 
+
+# Material and Methods
+
+## Simulations
 ~~~~~~
 java -jar invade.jar cluster --min-w 0.1 --genome mb:1 --rr cm_mb:4 --u 0.1 --N 1000 --gen 100 --basepop seg:10 --rep 500 --silent --steps 1 --cluster-insertions 1 --simid "1"  > test-s10.txt 
 ~~~~~~
+
+## Visualization

 We visualized the observed and the expected invasion with the following R-code

@@ -38,13 +53,3 @@
 gl<-ggplot()+geom_line(data=t,aes(x=gen,group=rep,y=tes*1000),alpha=0.15,size=0.3)+scale_y_log10()+geom_line(data=theo,aes(x=x,y=y),size=2)+theme(legend.position="none")+ylab("TE copies in population")+xlab("generation")
 plot(gl)
 ~~~~~~
-
-Which yields the following results:
-[[img src=obs-exp-inv.png]]
-
-* bold line: expectations based on the equation shown above
-* grey lines: observed invasions for 500 replicates
-
-
-## Conclusion
-Invade accurately reproduces the expected exponential increase of TE copy numbers in a population (no piRNA clusters).

Invasion modified by Robert Kofler

Robert Kofler — Wed, 06 Feb 2019 10:31:34 -0000

Invasion modified by Robert Kofler

Robert Kofler — Wed, 06 Feb 2019 10:31:15 -0000

--- v9
+++ v10
@@ -47,4 +47,4 @@

 ## Conclusion
-In the absence of piRNA-clusters Invade accurately reproduces the expected exponential increase of TE copy numbers in a population.
+Invade accurately reproduces the expected exponential increase of TE copy numbers in a population (no piRNA clusters).

Invasion modified by Robert Kofler

Robert Kofler — Wed, 06 Feb 2019 10:20:51 -0000

--- v8
+++ v9
@@ -41,3 +41,10 @@

 Which yields the following results:
 [[img src=obs-exp-inv.png]]
+
+* bold line: expectations based on the equation shown above
+* grey lines: observed invasions for 500 replicates
+
+
+## Conclusion
+In the absence of piRNA-clusters Invade accurately reproduces the expected exponential increase of TE copy numbers in a population.

Invasion modified by Robert Kofler

Robert Kofler — Wed, 06 Feb 2019 10:18:49 -0000

Invasion modified by Robert Kofler

Robert Kofler — Wed, 06 Feb 2019 10:18:18 -0000

Invasion modified by Robert Kofler

Robert Kofler — Wed, 06 Feb 2019 10:10:15 -0000

--- v5
+++ v6
@@ -37,5 +37,7 @@

 gl<-ggplot()+geom_line(data=t,aes(x=gen,group=rep,y=tes*1000),alpha=0.15,size=0.3)+scale_y_log10()+geom_line(data=theo,aes(x=x,y=y),size=2)+theme(legend.position="none")+ylab("TE copies in population")+xlab("generation")
 plot(gl)
+~~~~~~

-~~~~~~
+Which yields the following results:
+[[img src=obs-exp-inv.png]]

Invasion modified by Robert Kofler

Robert Kofler — Wed, 06 Feb 2019 10:09:00 -0000

--- v4
+++ v5
@@ -18,3 +18,24 @@
 ~~~~~~
 java -jar invade.jar cluster --min-w 0.1 --genome mb:1 --rr cm_mb:4 --u 0.1 --N 1000 --gen 100 --basepop seg:10 --rep 500 --silent --steps 1 --cluster-insertions 1 --simid "1"  > test-s10.txt 
 ~~~~~~
+
+We visualized the observed and the expected invasion with the following R-code
+
+~~~~~~
+library(ggplot2)
+library(RColorBrewer)
+library(plyr)
+library(gridExtra)
+theme_set(theme_bw())
+
+cn<-seq(0,99,1)
+res<-10*1.1^cn
+theo<-data.frame(x=1:100,y=res)
+t<-read.table("test-s10.txt")
+names(t)<-c("rep","gen","c1","c2","c3","tes")
+t$rep<-as.factor(t$rep)
+
+gl<-ggplot()+geom_line(data=t,aes(x=gen,group=rep,y=tes*1000),alpha=0.15,size=0.3)+scale_y_log10()+geom_line(data=theo,aes(x=x,y=y),size=2)+theme(legend.position="none")+ylab("TE copies in population")+xlab("generation")
+plot(gl)
+
+~~~~~~

Invasion modified by Robert Kofler

Robert Kofler — Wed, 06 Feb 2019 10:06:38 -0000

--- v3
+++ v4
@@ -13,7 +13,7 @@

 We tested if a simulated invasion reproduces this expectations.
 We used a transposition rate of u=0.1 a population size of N=1000, a starting number of TEs of c0=10 and simulated the invasion for 100 generations. 
-A chromosome of size 1Mb and no piRNA clusters were simulated.
+A chromosome of size 1Mb and no piRNA clusters were simulated. We used 500 replicates.

 ~~~~~~
 java -jar invade.jar cluster --min-w 0.1 --genome mb:1 --rr cm_mb:4 --u 0.1 --N 1000 --gen 100 --basepop seg:10 --rep 500 --silent --steps 1 --cluster-insertions 1 --simid "1"  > test-s10.txt