Commit 3b3b302d authored by Beatriz Vicoso's avatar Beatriz Vicoso
Browse files

Update microsynteny.md

parent e00f3dbb
......@@ -33,3 +33,122 @@ cat Barb_Carp_1to2_exhaust_correctChrom.txt | awk '{print $3, $5}' | sort | join
## Plot in R
<details><summary>R commands for the plot are here.</summary>
```
synt<-read.table("~/Documents/Will/Carp2022/Microsynteny/SubA_SubB_coordinate.txt", head=F, sep=" ")
colnames(synt)<-c("subA", "scafA", "chromA", "coordA", "subB", "scafB", "chromB", "coordB")
synt$coordA<-(synt$coordA/10^6)
synt$coordB<-(synt$coordB/10^6)
head(synt)
par(mfrow=c(5,5))
par(mar=c(4,4,1,1))
par(mgp=c(1.8,0.8,0))
xlabplot<-"SubA coordinate (MB)"
ylabplot<-"SubB coordinate (MB)"
colplot<-"#1F78B4"
###chr1
subchrom<-subset(synt, chromA=="A1")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 1")
###chr2
subchrom<-subset(synt, chromA=="A2")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 2")
###chr3
subchrom<-subset(synt, chromA=="A3")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 3")
###chr4
subchrom<-subset(synt, chromA=="A4")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 4")
###chr5
subchrom<-subset(synt, chromA=="A5")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 5")
###chr6
subchrom<-subset(synt, chromA=="A6")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 6")
###chr7
subchrom<-subset(synt, chromA=="A7")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 7")
###chr8
subchrom<-subset(synt, chromA=="A8")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 8")
###chr9
subchrom<-subset(synt, chromA=="A9")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 9")
###chr10
subchrom<-subset(synt, chromA=="A10")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 10")
###chr11
subchrom<-subset(synt, chromA=="A11")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 11")
###chr12
subchrom<-subset(synt, chromA=="A12")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 12")
###chr13
subchrom<-subset(synt, chromA=="A13")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 13")
###chr14
subchrom<-subset(synt, chromA=="A14")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 14")
###chr15
subchrom<-subset(synt, chromA=="A15")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 15")
###chr16
subchrom<-subset(synt, chromA=="A16")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 16")
###chr17
subchrom<-subset(synt, chromA=="A17")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 17")
###chr18
subchrom<-subset(synt, chromA=="A18")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 18")
###chr19
subchrom<-subset(synt, chromA=="A19")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 19")
###chr20
subchrom<-subset(synt, chromA=="A20")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 20")
###chr21
subchrom<-subset(synt, chromA=="A21")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 21")
###chr22
subchrom<-subset(synt, chromA=="A22")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 22")
###chr23
subchrom<-subset(synt, chromA=="A23")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 23")
###chr24
subchrom<-subset(synt, chromA=="A24")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 24")
###chr25
subchrom<-subset(synt, chromA=="A25")
plot(subchrom$coordA, subchrom$coordB, pch=20, xlab= xlabplot, ylab= ylabplot, col= colplot, main="Chr. 25")
```
</details>
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