Commit 5057e5b9 authored by Beatriz Vicoso's avatar Beatriz Vicoso
Browse files

Update BarbCarpSynteny.md

parent 3b34974b
......@@ -65,5 +65,22 @@ B16 | B16 | 301
--> 5684/5833 genes (97%) are assigned to the same chromosomal element.
## Plot in R
```
synt<-read.table("~/Documents/Will/Carp2022/Revisions/BarbSynteny/PuntiusRNA_carpChr_PtetraChr.txt", head=F, sep=" ")
colnames(synt)<-c("Transcript", "CarpChr", "PtetraChr")
#synt$CarpChr<-gsub("B", "", synt$CarpChr)
#synt<-synt[order(as.numeric(gsub("B", "", synt$CarpChr))),]
final<-table(synt[,-1])
library(gplots)
heatmap.2(final, col= colorRampPalette(c("blue", "white", "red", "firebrick4"))(15), scale="none", margins = c(4,4), xlab="P.tetrazona Chromosome", ylab="Carp chromosome", trace="none", dendrogram="none", Rowv = F, Colv=F, key=T, lmat=( matrix(c(1,1,1, 2,4,3), nrow=2, byrow=TRUE) ), lwid=c(1.5, 4, 2 ), lhei=c(4.2, 1 ), key.title=NA, key.xlab="Gene Number", cellnote = final)
```
The figure is here:
<img src="images/BarbCarpSynteny_heatmap.jpg" width=500>
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment