Figure 5B

Setup

3way_planes_CFU.xlsx

# Lamberti: Fig 5 and related. Comparing lower dimensional bacterial interactions for various phenotypes.

library(readxl)

0.5s

Rmicrobiome r env

readxl, gdtools, svglite, ....

X3way_planes_CFU <- read_excel(3way_planes_CFU.xlsx↩)
attach(X3way_planes_CFU)

1.5s

Rmicrobiome r env

Analysis

0.4s

Rmicrobiome r env

# **klm t(planes_CFU)

plot(t(X3way_planes_CFU[1,c(2,5,8,11,14,17)]), pch=c(0,1,2,4,8,5,6),  
     xlim=c(1,6) , ylim=c(-800000,800000), col = "black", ylab=" ",xlab=" ", axes = FALSE)
title("**klm", line = 1)
x<-1:6
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="Index",cex=0.65, line=3)
mtext(side=2,text="Interaction (CFUs)", cex=0.65, line=5)
points(t(X3way_planes_CFU[2,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "red")
points(t(X3way_planes_CFU[3,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "blue")
points(t(X3way_planes_CFU[4,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "green3")
abline(h =0,lty = "dashed", col = "grey")


arrows(x,t(X3way_planes_CFU[1,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[1,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[1,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[1,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, lty=3)
arrows(x,t(X3way_planes_CFU[2,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[2,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[2,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[2,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col= "red",lty=3)
arrows(x,t(X3way_planes_CFU[3,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[3,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[3,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[3,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="blue",lty=3)
arrows(x,t(X3way_planes_CFU[4,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[4,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[4,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[4,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="green3",lty=3)

legend("topleft",
       legend=c("AB***", "A*B**", "A**B*", "A***B", "*AB**", "*A*B*","*A**B","**AB*","**A*B","***AB"), 
       pch =c(0,1,2,4,8,5,6,10,11,12), 
)
legend("topright",
       legend=c("bystander 00","bystander 01","bystander 10","bystander 11" ),
       col = c("black","red","blue","green"),pch=16)

0.4s

Rmicrobiome r env

list(w = 1.47039076861213,....

0.5s

Rmicrobiome r env

# *k*lm t(planes_CFU)
plot(  t(X3way_planes_CFU[6,c(2,5,8,11,14,17)]), pch=c(0,1,2,4,8,5,6),  
       xlim=c(1,6) , ylim=c(-800000,800000), col = "black",ylab=" ",xlab=" ", axes = FALSE)
title("*k*lm", line = 1)
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="Index",cex=0.65, line=3)
points(t(X3way_planes_CFU[7,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "red")
points(t(X3way_planes_CFU[8,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "blue")
points(t(X3way_planes_CFU[9,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "green3")
abline(h =0,lty = "dashed", col = "grey")

arrows(x,t(X3way_planes_CFU[6,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[6,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[6,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[6,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, lty=3)
arrows(x,t(X3way_planes_CFU[7,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[7,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[7,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[7,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col= "red",lty=3)
arrows(x,t(X3way_planes_CFU[8,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[8,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[8,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[8,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="blue",lty=3)
arrows(x,t(X3way_planes_CFU[9,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[9,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[9,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[9,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="green3",lty=3)

legend("topleft",
       legend=c("AB***", "A*B**", "A**B*", "A***B", "*AB**", "*A*B*","*A**B","**AB*","**A*B","***AB"), 
       pch =c(0,1,2,4,8,5,6,10,11,12), 
)
legend("topright",
       legend=c("bystander 00","bystander 01","bystander 10","bystander 11" ),
       col = c("black","red","blue","green"),pch=16)

0.5s

Rmicrobiome r env

list(w = 1.47039076861213,....

0.6s

Rmicrobiome r env

# **klm t(planes_CFU)
plot(  t(X3way_planes_CFU[11,c(2,5,8,11,14,17)]), pch=c(0,1,2,4,8,5,6),  xlim=c(1,6) , ylim=c(-800000,800000), col = "black", 
       ylab=" ",xlab=" ", axes = FALSE)
title("*kl*m", line = 1)
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="Index",cex=0.65, line=3)
points(t(X3way_planes_CFU[12,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "red")
points(t(X3way_planes_CFU[13,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "blue")
points(t(X3way_planes_CFU[14,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "green3")
abline(h =0,lty = "dashed", col = "grey")

arrows(x,t(X3way_planes_CFU[11,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[11,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[11,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[11,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, lty=3)
arrows(x,t(X3way_planes_CFU[12,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[12,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[12,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[12,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col= "red",lty=3)
arrows(x,t(X3way_planes_CFU[13,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[13,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[13,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[13,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="blue",lty=3)
arrows(x,t(X3way_planes_CFU[14,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[14,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[14,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[14,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="green3",lty=3)

legend("topleft",
       legend=c("AB***", "A*B**", "A**B*", "A***B", "*AB**", "*A*B*","*A**B","**AB*","**A*B","***AB"), 
       pch =c(0,1,2,4,8,5,6,10,11,12), 
)
legend("topright",
       legend=c("bystander 00","bystander 01","bystander 10","bystander 11" ),
       col = c("black","red","blue","green"),pch=16)

0.6s

Rmicrobiome r env

list(w = 1.47039076861213,....

0.4s

Rmicrobiome r env

# **klm t(planes_CFU)
plot(  t(X3way_planes_CFU[16,c(2,5,8,11,14,17)]), pch=c(0,1,2,4,8,5,6),  xlim=c(1,6) , ylim=c(-800000,800000), col = "black", 
       ylab=" ",xlab=" ", axes = FALSE)
title("*klm*", line = 1)
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="Index",cex=0.65, line=3)
points(t(X3way_planes_CFU[17,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "red")
points(t(X3way_planes_CFU[18,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "blue")
points(t(X3way_planes_CFU[19,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "green3")
abline(h =0,lty = "dashed", col = "grey")

arrows(x,t(X3way_planes_CFU[16,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[16,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[16,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[16,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, lty=3)
arrows(x,t(X3way_planes_CFU[17,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[17,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[17,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[17,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col= "red",lty=3)
arrows(x,t(X3way_planes_CFU[18,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[18,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[18,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[18,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="blue",lty=3)
arrows(x,t(X3way_planes_CFU[19,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[19,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[19,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[19,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="green3",lty=3)

legend("topleft",
       legend=c("AB***", "A*B**", "A**B*", "A***B", "*AB**", "*A*B*","*A**B","**AB*","**A*B","***AB"), 
       pch =c(0,1,2,4,8,5,6,10,11,12), 
)
legend("topright",
       legend=c("bystander 00","bystander 01","bystander 10","bystander 11" ),
       col = c("black","red","blue","green"),pch=16)

0.4s

Rmicrobiome r env

list(w = 1.47039076861213,....

0.5s

Rmicrobiome r env

# **klm t(planes_CFU)
plot(  t(X3way_planes_CFU[21,c(2,5,8,11,14,17)]), pch=c(0,1,2,4,8,5,6),  xlim=c(1,6) , ylim=c(-800000,800000), col = "black", 
       ylab=" ",xlab=" ", axes = FALSE)
title("k**lm", line = 1)
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="Index",cex=0.65, line=3)
points(t(X3way_planes_CFU[22,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "red")
points(t(X3way_planes_CFU[23,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "blue")
points(t(X3way_planes_CFU[24,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "green3")
abline(h =0,lty = "dashed", col = "grey")

arrows(x,t(X3way_planes_CFU[21,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[21,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[21,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[21,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, lty=3)
arrows(x,t(X3way_planes_CFU[22,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[22,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[22,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[22,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col= "red",lty=3)
arrows(x,t(X3way_planes_CFU[23,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[23,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[23,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[23,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="blue",lty=3)
arrows(x,t(X3way_planes_CFU[24,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[24,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[24,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[24,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="green3",lty=3)

legend("topleft",
       legend=c("AB***", "A*B**", "A**B*", "A***B", "*AB**", "*A*B*","*A**B","**AB*","**A*B","***AB"), 
       pch =c(0,1,2,4,8,5,6,10,11,12), 
)
legend("topright",
       legend=c("bystander 00","bystander 01","bystander 10","bystander 11" ),
       col = c("black","red","blue","green"),pch=16)

0.5s

Rmicrobiome r env

list(w = 1.47039076861213,....

0.5s

Rmicrobiome r env

# **klm  t(planes_CFU)

plot(  t(X3way_planes_CFU[26,c(2,5,8,11,14,17)]), pch=c(0,1,2,4,8,5,6),  xlim=c(1,6) , ylim=c(-800000,800000), col = "black",
       ylab=" ",xlab=" ", axes = FALSE)
title("k*l*m", line = 1)
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="Index",cex=0.65, line=3)
points(t(X3way_planes_CFU[27,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "red")
points(t(X3way_planes_CFU[28,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "blue")
points(t(X3way_planes_CFU[29,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "green3")
abline(h =0,lty = "dashed", col = "grey")

arrows(x,t(X3way_planes_CFU[26,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[26,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[26,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[26,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, lty=3)
arrows(x,t(X3way_planes_CFU[27,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[27,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[27,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[27,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col= "red",lty=3)
arrows(x,t(X3way_planes_CFU[28,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[28,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[28,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[28,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="blue",lty=3)
arrows(x,t(X3way_planes_CFU[29,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[29,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[29,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[29,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="green3",lty=3)

legend("topleft",
       legend=c("AB***", "A*B**", "A**B*", "A***B", "*AB**", "*A*B*","*A**B","**AB*","**A*B","***AB"), 
       pch =c(0,1,2,4,8,5,6,10,11,12), 
)
legend("topright",
       legend=c("bystander 00","bystander 01","bystander 10","bystander 11" ),
       col = c("black","red","blue","green"),pch=16)

0.5s

Rmicrobiome r env

list(w = 1.47039076861213,....

0.5s

Rmicrobiome r env

# **klm  t(planes_CFU)

plot(  t(X3way_planes_CFU[31,c(2,5,8,11,14,17)]), pch=c(0,1,2,4,8,5,6),  xlim=c(1,6) , ylim=c(-800000,800000), col = "black", 
       ylab=" ",xlab=" ", axes = FALSE)
title("k*lm*", line = 1)
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="Index",cex=0.65, line=3)
points(t(X3way_planes_CFU[32,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "red")
points(t(X3way_planes_CFU[33,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "blue")
points(t(X3way_planes_CFU[34,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "green3")
abline(h =0,lty = "dashed", col = "grey")

arrows(x,t(X3way_planes_CFU[31,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[31,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[31,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[31,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, lty=3)
arrows(x,t(X3way_planes_CFU[32,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[32,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[32,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[32,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col= "red",lty=3)
arrows(x,t(X3way_planes_CFU[33,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[33,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[33,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[33,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="blue",lty=3)
arrows(x,t(X3way_planes_CFU[34,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[34,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[34,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[34,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="green3",lty=3)

legend("topleft",
       legend=c("AB***", "A*B**", "A**B*", "A***B", "*AB**", "*A*B*","*A**B","**AB*","**A*B","***AB"), 
       pch =c(0,1,2,4,8,5,6,10,11,12), 
)
legend("topright",
       legend=c("bystander 00","bystander 01","bystander 10","bystander 11" ),
       col = c("black","red","blue","green"),pch=16)

0.5s

Rmicrobiome r env

list(w = 1.47039076861213,....

0.4s

Rmicrobiome r env

# **klm  t(planes_CFU)

plot(  t(X3way_planes_CFU[36,c(2,5,8,11,14,17)]), pch=c(0,1,2,4,8,5,6),  xlim=c(1,6) , ylim=c(-800000,800000), col = "black", 
       ylab=" ",xlab=" ", axes = FALSE)
title("kl**m", line = 1)
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="Index",cex=0.65, line=3)
points(t(X3way_planes_CFU[37,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "red")
points(t(X3way_planes_CFU[38,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "blue")
points(t(X3way_planes_CFU[39,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "green3")
abline(h =0,lty = "dashed", col = "grey")

arrows(x,t(X3way_planes_CFU[36,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[36,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[36,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[36,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, lty=3)
arrows(x,t(X3way_planes_CFU[37,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[37,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[37,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[37,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col= "red",lty=3)
arrows(x,t(X3way_planes_CFU[38,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[38,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[38,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[38,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="blue",lty=3)
arrows(x,t(X3way_planes_CFU[39,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[39,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[39,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[39,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="green3",lty=3)

legend("topleft",
       legend=c("AB***", "A*B**", "A**B*", "A***B", "*AB**", "*A*B*","*A**B","**AB*","**A*B","***AB"), 
       pch =c(0,1,2,4,8,5,6,10,11,12), 
)
legend("topright",
       legend=c("bystander 00","bystander 01","bystander 10","bystander 11" ),
       col = c("black","red","blue","green"),pch=16)

0.4s

Rmicrobiome r env

list(w = 1.47039076861213,....

0.3s

Rmicrobiome r env

# **klm  t(planes_CFU)

plot(  t(X3way_planes_CFU[41,c(2,5,8,11,14,17)]), pch=c(0,1,2,4,8,5,6),  xlim=c(1,6) , ylim=c(-800000,800000), col = "black", 
       ylab=" ",xlab=" ", axes = FALSE)
title("kl*m*", line = 1)
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="Index",cex=0.65, line=3)
points(t(X3way_planes_CFU[42,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "red")
points(t(X3way_planes_CFU[43,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "blue")
points(t(X3way_planes_CFU[44,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "green3")
abline(h =0,lty = "dashed", col = "grey")

arrows(x,t(X3way_planes_CFU[41,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[41,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[41,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[41,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, lty=3)
arrows(x,t(X3way_planes_CFU[42,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[42,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[42,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[42,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col= "red",lty=3)
arrows(x,t(X3way_planes_CFU[43,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[43,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[43,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[43,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="blue",lty=3)
arrows(x,t(X3way_planes_CFU[44,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[44,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[44,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[44,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="green3",lty=3)

legend("topleft",
       legend=c("AB***", "A*B**", "A**B*", "A***B", "*AB**", "*A*B*","*A**B","**AB*","**A*B","***AB"), 
       pch =c(0,1,2,4,8,5,6,10,11,12), 
)
legend("topright",
       legend=c("bystander 00","bystander 01","bystander 10","bystander 11" ),
       col = c("black","red","blue","green"),pch=16)

0.3s

Rmicrobiome r env

list(w = 1.47039076861213,....

0.4s

Rmicrobiome r env

# **klm  t(planes_CFU)

plot(  t(X3way_planes_CFU[46,c(2,5,8,11,14,17)]), pch=c(0,1,2,4,8,5,6),  xlim=c(1,6) , ylim=c(-800000,800000), col = "black", 
       ylab=" ",xlab=" ", axes = FALSE)
title("klm**", line = 1)
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="Index",cex=0.65, line=3)
points(t(X3way_planes_CFU[47,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "red")
points(t(X3way_planes_CFU[48,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "blue")
points(t(X3way_planes_CFU[49,c(2,5,8,11,14,17)]),pch=c(0,1,2,4,8,5,6),col = "green3")
abline(h =0,lty = "dashed", col = "grey")

arrows(x,t(X3way_planes_CFU[46,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[46,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[46,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[46,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, lty=3)
arrows(x,t(X3way_planes_CFU[47,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[47,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[47,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[47,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col= "red",lty=3)
arrows(x,t(X3way_planes_CFU[48,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[48,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[48,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[48,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="blue",lty=3)
arrows(x,t(X3way_planes_CFU[49,c(2,5,8,11,14,17)])-t(X3way_planes_CFU[49,c(3,6,9,12,15,18)]), x,
       t(X3way_planes_CFU[49,c(2,5,8,11,14,17)])+t(X3way_planes_CFU[49,c(3,6,9,12,15,18)]), 
       length=0.05, angle=90, code=3, col="green3",lty=3)

legend("topleft",
       legend=c("AB***", "A*B**", "A**B*", "A***B", "*AB**", "*A*B*","*A**B","**AB*","**A*B","***AB"), 
       pch =c(0,1,2,4,8,5,6,10,11,12), 
)
legend("topright",
       legend=c("bystander 00","bystander 01","bystander 10","bystander 11" ),
       col = c("black","red","blue","green"),pch=16)

0.4s

Rmicrobiome r env

list(w = 1.47039076861213,....