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Copy pathAmbALSmo_mapGeno.R
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AmbALSmo_mapGeno.R
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##############################################################################/
##############################################################################/
#Figure 1: code for plotting the maps of the genotypes
##############################################################################/
##############################################################################/
#loading the necessary packages and data
source("AmbALSmo_load.R")
#load the results of the high throughput sequencing monitoring
databruteTOT<-read.delim(
"data/data_carto_france.txt",
header=TRUE,
sep="\t",
colClasses=c("character","numeric","numeric",
"numeric","numeric","numeric","numeric",
"numeric","numeric","numeric","numeric",
"numeric","numeric","numeric","factor",
"factor","factor","factor")
)
databruteTOT$RS<-rowSums(databruteTOT[,4:14])
levels(databruteTOT$SeqMeth)<-c(21,24)
#turning this dataframe into a spatial dataframe (wgs84)
ambro.wgs<-SpatialPointsDataFrame(coords=databruteTOT[,c(3,2)],
data=databruteTOT,
proj4string=CRS("+proj=longlat +datum=WGS84")
)
ambro<-spTransform(ambro.wgs,CRS("+init=epsg:2154"))
##############################################################################/
#code for the maps by mutation in WGS####
##############################################################################/
#each position on separate map
op<-par(mar=c(0,0,1,0),mfrow=c(2,3))
#position 197
plot(DEP_SHP,lwd=0.8,border=grey(0.7),
main="ALS codon 197")
plot(REG_SHP,lwd=1.8,add=TRUE)
plot(ambro,pch=as.numeric(as.character(ambro$SeqMeth)),
col="transparent",
bg=rgb(50,100,0,150,maxColorValue=255),cex=1.1,
add=TRUE)
plot(ambro[ambro@data[,6]!=0,],
pch=as.numeric(as.character(ambro[ambro@data[,6]!=0,]$SeqMeth)),
bg="red",cex=1.5,
add=TRUE)
plot(ambro[ambro@data[,10]!=0,],
pch=as.numeric(as.character(ambro[ambro@data[,10]!=0,]$SeqMeth)),
bg="blue",cex=1.5,
add=TRUE)
plot(ambro[ambro@data[,11]!=0,],
pch=as.numeric(as.character(ambro[ambro@data[,11]!=0,]$SeqMeth)),
bg="purple",cex=1.5,
add=TRUE)
legend(57000,7160000,
legend=c("No mutation at 197","Gln197","Ser197","Thr197"),
cex=1,pt.cex=1.8,
y.intersp=0.5,x.intersp=0.5,
pch=15,col=c(rgb(50,100,0,150,maxColorValue=255),
"red","blue","purple"),bg="transparent",bty="n")
legend(850000,7160000,legend=c("Sanger","NGS"),cex=1,pt.cex=1.6,
y.intersp=0.5,x.intersp=0.5,
pch=c(2,1),col=c("black"),bg="transparent",bty="n")
scalebar(c(191260,6060000),300000,"km",division.cex=1)
#position 205
plot(DEP_SHP,lwd=0.8,border=grey(0.7),
main="ALS codon 205")
plot(REG_SHP,lwd=1.8,add=TRUE)
plot(ambro,pch=as.numeric(as.character(ambro$SeqMeth)),
col="transparent",
bg=rgb(50,100,0,150,maxColorValue=255),cex=1.1,
add=TRUE)
plot(ambro[ambro@data[,12]!=0,],
pch=as.numeric(as.character(ambro[ambro@data[,12]!=0,]$SeqMeth)),
bg="red",cex=1.5,
add=TRUE)
plot(ambro[ambro@data[,13]!=0,],
pch=as.numeric(as.character(ambro[ambro@data[,13]!=0,]$SeqMeth)),
bg="blue",cex=1.5,
add=TRUE)
plot(ambro[ambro@data[,14]!=0,],
pch=as.numeric(as.character(ambro[ambro@data[,13]!=0,]$SeqMeth)),
bg="purple",cex=1.5,
add=TRUE)
legend(57000,7160000,
legend=c("No mutation at 205","Thr205.1","Thr205.2","Val205"),
cex=1,pt.cex=1.8,y.intersp=0.5,x.intersp=0.5,
pch=15,col=c(rgb(50,100,0,150,maxColorValue=255),
"red","blue","purple"),bg="transparent",bty="n")
legend(850000,7160000,legend=c("Sanger","NGS"),cex=1,pt.cex=1.6,
y.intersp=0.5,x.intersp=0.5,
pch=c(2,1),col=c("black"),bg="transparent",bty="n")
scalebar(c(191260,6060000),300000,"km",division.cex=1)
#position 376
plot(DEP_SHP,lwd=0.8,border=grey(0.7),
main="ALS codon 376")
plot(REG_SHP,lwd=1.8,add=TRUE)
plot(ambro,pch=as.numeric(as.character(ambro$SeqMeth)),
col="transparent",
bg=rgb(50,100,0,150,maxColorValue=255),cex=1.1,
add=TRUE)
plot(ambro[ambro@data[,7]!=0,],
pch=as.numeric(as.character(ambro[ambro@data[,7]!=0,]$SeqMeth)),
bg="red",cex=1.5,
add=TRUE)
legend(57000,7160000,
legend=c("No mutation at 376","Glu376"),cex=1,pt.cex=1.8,
y.intersp=0.5,x.intersp=0.5,
pch=15,col=c(rgb(50,100,0,150,maxColorValue=255),"red"),
bg="transparent",bty="n")
legend(850000,7160000,legend=c("Sanger","NGS"),cex=1,pt.cex=1.6,
y.intersp=0.5,x.intersp=0.5,
pch=c(2,1),col=c("black"),bg="transparent",bty="n")
scalebar(c(191260,6060000),300000,"km",division.cex=1)
#position 574
plot(DEP_SHP,lwd=0.8,border=grey(0.7),
main="ALS codon 574")
plot(REG_SHP,lwd=1.8,add=TRUE)
plot(ambro,pch=as.numeric(as.character(ambro$SeqMeth)),
col="transparent",
bg=rgb(50,100,0,150,maxColorValue=255),cex=1.1,
add=TRUE)
plot(ambro[ambro@data[,4]!=0,],
pch=as.numeric(as.character(ambro[ambro@data[,4]!=0,]$SeqMeth)),
bg="red",cex=1.5,
add=TRUE)
plot(ambro[ambro@data[,9]!=0,],
pch=as.numeric(as.character(ambro[ambro@data[,9]!=0,]$SeqMeth)),
bg="blue",cex=1.5,
add=TRUE)
legend(57000,7160000,
legend=c("No mutation at 574","Arg574","Leu574"),cex=1,pt.cex=1.8,
y.intersp=0.5,x.intersp=0.5,
pch=15,col=c(rgb(50,100,0,150,maxColorValue=255),"red","blue"),
bg="transparent",bty="n")
legend(850000,7160000,legend=c("Sanger","NGS"),cex=1,pt.cex=1.6,
y.intersp=0.5,x.intersp=0.5,
pch=c(2,1),col=c("black"),bg="transparent",bty="n")
scalebar(c(191260,6060000),300000,"km",division.cex=1)
#position 578
plot(DEP_SHP,lwd=0.8,border=grey(0.7),
main="ALS codon 578")
plot(REG_SHP,lwd=1.8,add=TRUE)
plot(ambro,pch=as.numeric(as.character(ambro$SeqMeth)),
col="transparent",
bg=rgb(50,100,0,150,maxColorValue=255),cex=1.1,
add=TRUE)
plot(ambro[ambro@data[,8]!=0,],
pch=as.numeric(as.character(ambro[ambro@data[,8]!=0,]$SeqMeth)),
bg="red",cex=1.5,
add=TRUE)
legend(57000,7160000,
legend=c("No mutation at 578","Ile578"),cex=1,pt.cex=1.8,
y.intersp=0.5,x.intersp=0.5,
pch=15,col=c(rgb(50,100,0,150,maxColorValue=255),"red"),
bg="transparent",bty="n")
scalebar(c(191260,6060000),300000,"km",division.cex=1)
legend(850000,7160000,legend=c("Sanger","NGS"),cex=1,pt.cex=1.6,
y.intersp=0.5,x.intersp=0.5,
pch=c(2,1),col=c("black"),bg="transparent",bty="n")
scalebar(c(191260,6060000),300000,"km",division.cex=1)
par(op)
#export to .pdf 12 x 7 inches
##############################################################################/
#END
##############################################################################/