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fusico_bioassay_ind.R
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fusico_bioassay_ind.R
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##############################################################################/
##############################################################################/
#R code for analyzing bioassays of Fusicoccum amygdali isolates
##############################################################################/
##############################################################################/
#loading the data
source("load_fusico_data.R")
##############################################################################/
#Regression analysis: mycelial growth experiment by individual isolates####
##############################################################################/
datafusamyIND<-datafusamy[datafusamy$strain_type!="population",]
#first we extract the list of the different SA listed in the file
SAlist<-levels(datafusamyIND$active_substance)
CompRez<-data.frame(Subs_Act=factor(),sample_ID=factor(),
EC50=character(),STERR=character())
#we make a subselection of the data according to the SA
for (j in 1:length(SAlist)) {
data_subSA<-datafusamyIND[datafusamyIND$active_substance==SAlist[j],]
#some individual never reach an inhibition of 50%, event for the highest
#tested concentration.
SA_rez<-as.character(data_subSA[data_subSA$dose==max(data_subSA$dose)
& data_subSA$perc_croiss>50,
"strain_ID"])
ifelse(length(SA_rez)==0,
REZSA<-data.frame(Subs_Act=factor(),sample_ID=factor(),
EC50=character(),STERR=character()),
REZSA<-data.frame("Subs_Act"=SAlist[j],"sample_ID"=SA_rez,
"EC50"=paste(">",max(data_subSA$dose),sep=""),
"STERR"="unknown"))
#we limit the dataset to the sample that reach somehow a EC of 50%
SA.dat<-data_subSA[!(data_subSA$strain_ID %in% SA_rez),]
SA.dat<-drop.levels(SA.dat)
for (i in 1:dim(table(SA.dat$strain_ID))[1]) {
temp.m1<-drm(perc_croiss~dose,
data=SA.dat[SA.dat$strain_ID==
names(table(SA.dat$strain_ID))[i],],
fct=LN.3())
plot(temp.m1,ylim=c(0,120),xlim=c(0,150),
main=paste(SAlist[j],names(table(SA.dat$strain_ID))[i]),
col.main=j)
temp<-ED(temp.m1,50,type="absolute")
tempx<-data.frame("Subs_Act"=SAlist[j],
"sample_ID"=names(table(SA.dat$strain_ID))[i],
"EC50"=as.character(temp[1]),
"STERR"=as.character(temp[2]))
REZSA<-rbind(REZSA,tempx)
}
CompRez<-rbind(CompRez,REZSA)
}
#adding a column for the population the individuals were isolated from
CompRez<-data.frame(CompRez,"popID"=as.factor(substr(CompRez$sample_ID,1,7)))
#exporting the result as a text file
write.table(CompRez, file="output/results_fusicoIND.txt",
sep="\t",quote=FALSE,row.names=FALSE)
##############################################################################/
#Figure 3A: Distribution of the carbendazim EC50 on isolates####
##############################################################################/
#preparing the data set, first we replace impossible value to compute by
#the highest dose used in the bioassay
CompRez$EC50<-as.numeric(as.character(CompRez$EC50))
CompRez[is.na(CompRez$EC50),"EC50"]<-100
CompRez$STERR<-as.numeric(as.character(CompRez$STERR))
CompRez[is.na(CompRez$STERR),"STERR"]<-0
carbenfi<-CompRez[CompRez$Subs_Act=="carbendazim",]
carbenfi<-carbenfi[order(as.numeric(as.character(carbenfi$EC50))),]
#computing the values for the whiskers
posi<-carbenfi[carbenfi$Subs_Act=="carbendazim",]$EC50+
carbenfi[carbenfi$Subs_Act=="carbendazim",]$STERR
negi<-carbenfi[carbenfi$Subs_Act=="carbendazim",]$EC50-
carbenfi[carbenfi$Subs_Act=="carbendazim",]$STERR
#because we can't plot CI that reach negative values in a plot
#with a log y-axes, we replace negative value by a very small value
negi[negi<0]<-0.001
#actual plotting
op<-par(mar=c(6.5,7,2,1),mfrow=c(2,1))
colov<-c("white","indianred1","black","dodgerblue")
plot(carbenfi[carbenfi$Subs_Act=="carbendazim",]$EC50,
log="y",las=1,ylim=c(0.005,100),bty="n",axes=FALSE,
ann=FALSE,col=colov[carbenfi$popID],
bg=c("black","white","white","dodgerblue")[carbenfi$popID],
pch=c(22,22,24,21)[carbenfi$popID],cex=1.5)
legend(45,35,col=colov,cex=1.5,x.intersp=0.5,y.intersp=0.4,
pt.bg=c("black","white","white","dodgerblue"),
legend=levels(carbenfi$popID),
pch=c(22,22,24,21),bty="n")
box(lwd=2.5,lty=1)
axis(1,at=c(0,10,20,30,40,50,60),
labels=c("0","10","20","30","40","50","60"),
cex.axis=1.3,font.axis=2,lwd.ticks=2)
axis(2,at=c(0.01,0.1,1,10,100),
labels=c("0.01","0.1","1","10",">100"),
cex.axis=1.3,font.axis=2,lwd.ticks=2,las=1)
title(xlab="Isolates arranged by carbendazim\nEC50 ascending order",
ylab="EC50 (mg/l)",
cex.lab=1.5,font.lab=2,line=5)
plotCI(c(1:63),
carbenfi[carbenfi$Subs_Act=="carbendazim",]$EC50,
ui=posi,
li=negi,
add=TRUE,cex=0.1,pch=21,col=rgb(0,0,0,1),pt.bg=rgb(0.7,0.7,0.7,1),
gap=0.00)
points(carbenfi[carbenfi$Subs_Act=="carbendazim",]$EC50,
pch=c(22,22,24,21)[carbenfi$popID],col=colov[carbenfi$popID],
bg=c("black","white","white","dodgerblue")[carbenfi$popID],
cex=1.5)
abline(h=50,lty=2,lwd=2)
text(-13,195,labels="(a)",cex=3,xpd=TRUE)
#export to .pdf 8 x 6 inches
##############################################################################/
#Figure 3B: Distribution of the diethofencarb EC50 on isolates####
##############################################################################/
#preparing the dataset, first we replace impossible value to compute by
#the highest dose used in the bioassay
CompRez$EC50<-as.numeric(as.character(CompRez$EC50))
CompRez[is.na(CompRez$EC50),"EC50"]<-100
CompRez$STERR<-as.numeric(as.character(CompRez$STERR))
CompRez[is.na(CompRez$STERR),"STERR"]<-0
diethofe<-CompRez[CompRez$Subs_Act=="diethofencarb",]
diethofe<-diethofe[order(as.numeric(as.character(diethofe$EC50))),]
#computing the values for the whiskers
posi<-diethofe[diethofe$Subs_Act=="diethofencarb",]$EC50+
diethofe[diethofe$Subs_Act=="diethofencarb",]$STERR
negi<-diethofe[diethofe$Subs_Act=="diethofencarb",]$EC50-
diethofe[diethofe$Subs_Act=="diethofencarb",]$STERR
#because we can't plot CI that reach negative values in a plot
#with a log y-axes, we replace negative value by a very small value
negi[negi<0]<-0.001
#actual plotting
colov<-c("white","indianred1","black","dodgerblue")
plot(diethofe[diethofe$Subs_Act=="diethofencarb",]$EC50,
log="y",las=1,ylim=c(0.005,100),bty="n",axes=FALSE,
ann=FALSE,col=colov[diethofe$popID],
bg=c("black","white","white","dodgerblue")[diethofe$popID],
pch=c(22,22,24,21)[diethofe$popID],cex=1.5)
box(lwd=2.5,lty=1)
axis(1,at=c(0,10,20,30,40,50,60),
labels=c("0","10","20","30","40","50","60"),
cex.axis=1.3,font.axis=2,lwd.ticks=2)
axis(2,at=c(0.01,0.1,1,10,100),
labels=c("0.01","0.1","1","10","100"),
cex.axis=1.3,font.axis=2,lwd.ticks=2,las=1)
title(xlab="Isolates arranged by diethofencarb\nEC50 ascending order",
ylab="EC50 (mg/l)",
cex.lab=1.5,font.lab=2,line=5)
plotCI(c(1:63),
diethofe[diethofe$Subs_Act=="diethofencarb",]$EC50,
ui=posi,li=negi,cex=0.1,pch=21,col=rgb(0,0,0,1),
pt.bg=rgb(0.7,0.7,0.7,1),gap=0.00,add=TRUE)
points(diethofe[diethofe$Subs_Act=="diethofencarb",]$EC50,
pch=c(22,22,24,21)[diethofe$popID],col=colov[diethofe$popID],
bg=c("black","white","white","dodgerblue")[diethofe$popID],
cex=1.5)
text(-13,195,labels="(b)",cex=3,xpd=TRUE)
par(op)
#export to .pdf 8 x 12 inches
##############################################################################/
#Figure SX: Correlation between EC50 carbendazim vs diethofencarb####
##############################################################################/
CarbVsDietho<-merge(carbenfi,diethofe,by="sample_ID")
op<-par(mar=c(6,6,2,1))
colov<-c("white","indianred1","black","dodgerblue")
plot(CarbVsDietho$EC50.y~CarbVsDietho$EC50.x,log="xy",bty="n",axes=FALSE,
xlim=c(0.01,100),ylim=c(10,100),las=1,ann=FALSE,
col=colov[CarbVsDietho$popID.x],
bg=c("black","white","white","dodgerblue")[CarbVsDietho$popID.x],
pch=c(22,22,24,21)[CarbVsDietho$popID.x],cex=1.5)
abline(v=50,lty=2,lwd=2)
legend(2,19,col=colov,cex=1.5,x.intersp=0.5,
pt.bg=c("black","white","white","dodgerblue"),
legend=levels(carbenfi$popID),
pch=c(22,22,24,21),bty="o",box.col="transparent",bg="transparent")
box(lwd=2.5,lty=1)
axis(1,at=c(0.01,0.1,1,10,100),
labels=c("0.01","0.1","1","10",">100"),
cex.axis=1.5,font.axis=2,lwd.ticks=2,las=1)
axis(2,at=c(10,20,40,70,100),
labels=c("10","20","40","70","100"),
cex.axis=1.5,font.axis=2,lwd.ticks=2,las=1)
title(xlab="Carbendazim EC50 (mg/l)",
ylab="Diethofencarb EC50 (mg/l)",
cex.lab=1.8,font.lab=2,line=3.5)
par(op)
#text(0.0017,116,labels="C",cex=4,xpd=TRUE)
#export to .pdf 8 x 6 inches
##############################################################################/
#Regression analysis: carbendazim and thiophanate mycelial bioassay####
##############################################################################/
datafusamyIND<-datatemp[datatemp$strain_type!="population",]
#first we extract the list of the different SA listed in the file
SAlist<-levels(datafusamyIND$active_substance)
CompRez<-data.frame(Subs_Act=factor(),sample_ID=factor(),
EC50=character(),STERR=character())
#we make a subselection of the data according to the SA
for (j in 1:length(SAlist)) {
data_subSA<-datafusamyIND[datafusamyIND$active_substance==SAlist[j],]
#some individual never reach an inhibition of 50%, event for the highest
#tested concentration.
SA_rez<-as.character(data_subSA[data_subSA$dose==max(data_subSA$dose)
& data_subSA$perc_croiss>50,
"strain_ID"])
ifelse(length(SA_rez)==0,
REZSA<-data.frame(Subs_Act=factor(),sample_ID=factor(),
EC50=character(),STERR=character()),
REZSA<-data.frame("Subs_Act"=SAlist[j],"sample_ID"=SA_rez,
"EC50"=paste(">",max(data_subSA$dose),sep=""),
"STERR"="unknown"))
#we limit the dataset to the sample that reach somehow a IC of 50%
SA.dat<-data_subSA[!(data_subSA$strain_ID %in% SA_rez),]
SA.dat<-drop.levels(SA.dat)
for (i in 1:dim(table(SA.dat$strain_ID))[1]) {
temp.m1<-drm(perc_croiss~dose,
data=SA.dat[SA.dat$strain_ID==
names(table(SA.dat$strain_ID))[i],],
fct=LN.3())
plot(temp.m1,ylim=c(0,120),xlim=c(0,450),
main=paste(SAlist[j],names(table(SA.dat$strain_ID))[i]),
col.main=j)
temp<-ED(temp.m1,50,type="absolute")
tempx<-data.frame("Subs_Act"=SAlist[j],
"sample_ID"=names(table(SA.dat$strain_ID))[i],
"EC50"=as.character(temp[1]),
"STERR"=as.character(temp[2]))
REZSA<-rbind(REZSA,tempx)
}
CompRez<-rbind(CompRez,REZSA)
}
#adding a column for the population the individuals were isolated from
CompRez<-data.frame(CompRez,"popID"=as.factor(substr(CompRez$sample_ID,1,7)))
#exporting the result as a text file
write.table(CompRez, file="output/results_fusitemp.txt",
sep="\t",quote=FALSE,row.names=FALSE)
##############################################################################/
#END
##############################################################################/