Figure 4 - Microbiome interactions change host physiology

# Fig4 B-E: Microbiome interactions (2,3,4,5 way interactions and 3D circuits) change host physiology - coloring as in main paper.
options(nextjournal.device.real = "svg")
library(yarrr)
library(readxl)

output_with_p <- read_excel(output_with_p.xlsx↩)
attach(output_with_p)

# CFU
e0<-CFU
e4<-`CFU sign`

d<-output_with_p[c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936),13]
d<-cbind(c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936), d)
colnames(d) <- c("x", "y")
d5<-output_with_p[c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936),17]
d5<-cbind(c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936), d5)
colnames(d5) <- c("x", "y")

b=min(CFU,na.rm=T)
e=max(CFU,na.rm=T)
plot(e0,main="Bacterial load (means)", pch=1,  xlim=c(0,926) , 
     ylim=c(b,e),
     col = transparent("deepskyblue", trans.val = .8),
     xlab = "",
     ylab = "",
     axes = FALSE)
box()
axis(1,at = NULL, labels =TRUE,lwd = 0.5) 
axis(2, at = NULL,labels=TRUE, lwd = 0.5, las=2)
mtext(side=1,text="Tests",cex=0.65, line=3)
mtext(side=2,text="Interaction (CFUs)", cex=0.65, line=5)
points(e4,pch=19,col = transparent("blue", trans.val = .35))
points(d$x, d$y,pch=1,col = "deeppink" )
points(d5$x, d5$y,pch=19,col = "deeppink4" )

abline(v = 320, untf = FALSE, col="black", lty = 3)
abline(v = 640, untf = FALSE, col="black", lty = 3)
abline(v = 800, untf = FALSE, col="black", lty = 3)
abline(v = 910, untf = FALSE, col="black", lty = 3)


#dev
e6<-`dev`
e8<-`dev sign`
d6<-output_with_p[c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936),3]
d6<-cbind(c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936), d6)
colnames(d6) <- c("x", "y")
d8<-output_with_p[c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936),7]
d8<-cbind(c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936), d8)
colnames(d8) <- c("x", "y")
b=min(dev,na.rm=T)
e=max(dev,na.rm=T)

plot(e6,main="Development time", pch=1,  xlim=c(0,926) , ylim=c(b,e),
     col = transparent("deepskyblue", trans.val = .8),
     xlab = "",
     ylab = "",
     axes = FALSE)
box()
axis(1,at = NULL, labels =TRUE,lwd = 0.5) 
axis(2, at = NULL,labels=TRUE, lwd = 0.5, las=2)
mtext(side=1,text="Tests",cex=0.65, line=3)
mtext(side=2,text="Interaction (Days)", cex=0.65, line=3)
points(e8,pch=19,col = transparent("blue", trans.val = .35))
points(d6$x,d6$y,pch=1,col = "deeppink" )
points(d8$x,d8$y,pch=19,col = "deeppink4" )


abline(v = 320, untf = FALSE, col="black", lty = 3)
abline(v = 640, untf = FALSE, col="black", lty = 3)
abline(v = 800, untf = FALSE, col="black", lty = 3)
abline(v = 910, untf = FALSE, col="black", lty = 3)



# fec
e11<-`fec`
e5<-`fec sign`
d<-output_with_p[c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936),8]
d<-cbind(c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936), d)
colnames(d) <- c("x", "y")
d5<-output_with_p[c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936),12]
d5<-cbind(c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936), d5)
colnames(d5) <- c("x", "y")
b=min(fec,na.rm=T)
e=max(fec,na.rm=T)

plot(e11,main="Daily fecundity", pch=1,  xlim=c(0,926) , ylim=c(b,e),
     col = transparent("deepskyblue", trans.val = .8),
     xlab = "",
     ylab = "",
     axes = FALSE)
box()
axis(1,at = NULL, labels =TRUE,lwd = 0.5) 
axis(2, at = NULL,labels=TRUE, lwd = 0.5, las=2)
mtext(side=1,text="Tests",cex=0.65, line=3)
mtext(side=2,text="Interaction (Offspring/day/female)", cex=0.65, line=3)
points(e5,pch=19,col = transparent("blue", trans.val = .35))
points(d$x,d$y,pch=1,col ="deeppink" )
points(d5$x,d5$y,pch=19,col ="deeppink4" )


abline(v = 320, untf = FALSE, col="black", lty = 3)
abline(v = 640, untf = FALSE, col="black", lty = 3)
abline(v = 800, untf = FALSE, col="black", lty = 3)
abline(v = 910, untf = FALSE, col="black", lty = 3)


# time d
d3<-`ttd`
e5<-`tts sign`
d<-output_with_p[c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936),18]
d <- cbind(c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936), d)
colnames(d) <- c("x", "y")
d5<-output_with_p[c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936),22]
d5<-cbind(c(1,5,9,15,19,25,49,53,59,73,761,765,769,773,777,781,785,789,793,797,901,903,905,907,909,936), d5)
colnames(d5) <- c("x", "y")
b=min(ttd,na.rm=T)
e=max(ttd,na.rm=T)

plot(d3,main="Time to death", pch=1 , xlim=c(0,926) , ylim=c(b,e),
     col = transparent("deepskyblue", trans.val = .8),
     xlab = "",
     ylab = "",
     axes = FALSE)
box()
axis(1,at = NULL, labels =TRUE,lwd = 0.5) 
axis(2, at = NULL,labels=TRUE, lwd = 0.5, las=2)
mtext(side=1,text="Tests",cex=0.65, line=3)
mtext(side=2,text="Interaction (days)", cex=0.65, line=3)
points(e5,pch=19,col =transparent("blue", trans.val = .35))
points(d$x,d$y,pch=1,col  ="deeppink" )
points(d5$x,d5$y,pch=19,col ="deeppink4" )

abline(v = 320, untf = FALSE, col="black", lty = 3)
abline(v = 640, untf = FALSE, col="black", lty = 3)
abline(v = 800, untf = FALSE, col="black", lty = 3)
abline(v = 910, untf = FALSE, col="black", lty = 3)



title("Scatter plot of all tested interactions \
      (for raw data)", outer=TRUE)