---
title: "GutlengthBoxplotsCumulativeAll Kruskal-Wallis & Dunn"
author: "Ben Jahnes"
date: "July 24, 2017"
output:
  pdf_document: default
  html_notebook: default
---
Import Data
```{r setup, include=FALSE}
setwd("D:/Documents/Manuscripts/Plots")

gutlength2<- read.csv("gutlength.cumulative.GF.GT.WT.csv", header =T,row.names=1)


#########################################################################
gutlength2$trt<-as.factor(gutlength2$trt)
gutlength2$Trt<-as.factor(gutlength2$Trt)
gutlength2$ind<-as.factor(gutlength2$ind)
gutlength2$ins<-as.factor(gutlength2$ins)
##gutlength$ins<-as.numeric(gutlength$ins)
Data=gutlength2

ins3<-Data[Data$ins=="3",]
ins6<-Data[Data$ins=="6",]


```

Import Libraries
```{r}
library(psych)
library(car)
library(MASS)
library(RColorBrewer)
library(FSA)
library(vioplot)
library(plyr)
library(dunn.test)
citation("dunn.test")
citation("FSA")
```


body Width Anova
```{r}
fitbw3<- aov(bw ~ Trt, data = Data[Data$ins=="3",])
fitbw4<- aov(bw ~ Trt, data = Data[Data$ins=="4",])
fitbw5<- aov(bw ~ Trt, data = Data[Data$ins=="5",])
summary(fitbw3)
summary(fitbw4)
summary(fitbw5)

fitbwtk3<-TukeyHSD(fitbw3, conf.level=.99);
fitbwtk4<-TukeyHSD(fitbw4, conf.level=.99);
fitbwtk5<-TukeyHSD(fitbw5, conf.level=.99);
fitbwtk3
fitbwtk4
fitbwtk5
```
Body Width Kruskal/Dunn
```{r}

kwbw<-kruskal.test(bw~ trt, data = Data[Data$ins==5,]) 

attach(Data[Data$ins==5,])
dunn.test(bw,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==5,])

#ins6<-wilcox.test(trt~ins, data = Data[Data$ins==6,])
```

insar 6 pairwise
```{r}
bw6<-ins6[complete.cases(ins6[ , 7]),]
bw6$trt<-droplevels(bw6$trt)
bw6$ins<-droplevels(bw6$ins)
bw6w<-wilcox.test(bw~trt, data = bw6)
bw6w
```


```{r}
Data.na.bw <-  Data[complete.cases(Data[ , 7]),]
nins3<-count(Data.na.bw$trt[Data.na.bw$ins==3])
nins4<-count(Data.na.bw$trt[Data.na.bw$ins==4])
nins5<-count(Data.na.bw$trt[Data.na.bw$ins==5])
nins6<-count(Data.na.bw$trt[Data.na.bw$ins==6])
nbw<-rbind(nins3, nins4, nins5, nins6)
nbwvec <- nbw$freq

```

body Width Boxplot
```{r}
#N<-c("n=","7","12","9","12","30","9","20","24","9","11","")
N<-c("n=",nbwvec,"","")
par(mfrow=c(1,1))

Data.na.bw <-  Data[complete.cases(Data[ , 7]),]
yrange <- range(Data.na.bw$bw)
wid=11.5

boxplot(bw~trt*ins,data=Data.na.bw,ylab="Width (mm)",outpch=NA, main="Body Width",varwidth=F, xlim=c(.5,wid),ylim=yrange,xaxt="n",col = c("palegreen4","steelblue","tomato"))
#text(.9, 9.8, paste("T-Test
#                    GF3-GT3 p=", round(bins3$p.value, 2), sep=""), cex=.7)
#text(.9, 9.4, paste("GF4-GT4 p=", round(bins4$p.value, 2), sep=""), cex=.7)
#text(.9, 9.1, paste("GF5-GT5 p=", round(bins5$p.value, 2), sep=""), cex=.7)
stripchart(bw~trt*ins, data = Data[Data$trt=="1",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="palegreen4", 
           add = TRUE)
stripchart(bw~trt*ins, data = Data[Data$trt=="2",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE)             
stripchart(bw~trt*ins, data = Data[Data$trt=="3",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato", 
           add = TRUE)
#stripchart(bw~trt, data = Data,   
#           vertical = TRUE, method = "jitter",    
#           pch = 21, col = "black", bg ="red", 
#           add = TRUE)


#stripchart(bw~trt, data = Data4[Data$trt=="1",],   
#           vertical = TRUE, method = "jitter",    
#           pch = 21, col = "black", bg ="red", 
#           add = TRUE)
#stripchart(bw~trt, data = Data4[Data$trt=="2",],   
#           vertical = TRUE, method = "jitter",    
#           pch = 21, col = "black", bg ="red", 
#           add = TRUE)             
#stripchart(bw~trt, data = Data4[Data$trt=="3",],   
#          vertical = TRUE, method = "jitter",    
#           pch = 21, col = "black", bg ="red", 
#           add = TRUE)

y=2

axis(1, at=seq(3.5,wid, by=3), labels = FALSE,xlab=F)
text(y=y,x= seq(2,wid, by=3), par("usr")[3] - 0.2, labels = c("Third", "Fourth", "Fifth","sixth"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
legend("topleft", inset=.05, c( "Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=1)
text(y=y-1,x= seq(0,wid, by=1), paste(labels=N,sep=""), srt = 0, xpd = TRUE, cex=1, font=1)
title(xlab="Instar", line=1.5, cex.lab=1)

```

Body Length Kruskal/Dunn
```{r}

kwbl<-kruskal.test(bl~ trt, data = Data[Data$ins==5,]) 

attach(Data[Data$ins==5,])
dunn.test(bl,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==5,])

#ins6<-wilcox.test(trt~ins, data = Data[Data$ins==3,])
```

Body Length Stats
```{r}
#fitb3<- aov(bl ~ Trt, data = Data[Data$ins=="3",])
fitb4<- aov(bl ~ Trt, data = Data[Data$ins=="4",])
fitb5<- aov(bl ~ Trt, data = Data[Data$ins=="5",])
#summary(fitb3)
summary(fitb4)
summary(fitb5)

#fitbtk3<-TukeyHSD(fitb3, conf.level=.99);
fitbtk4<-TukeyHSD(fitb4, conf.level=.99);
fitbtk5<-TukeyHSD(fitb5, conf.level=.99);
#fitbtk3
fitbtk4
fitbtk5

```
insar 6 pairwise
```{r}
bl6<-ins6[complete.cases(ins6[ , 8]),]
bl6$trt<-droplevels(bl6$trt)
bl6$ins<-droplevels(bl6$ins)
bl6w<-wilcox.test(bl~trt, data = bl6)
bl6w
```

```{r}
Data.na.bl <-  Data[complete.cases(Data[ , 8]),]
nins3<-count(Data.na.bl$trt[Data.na.bl$ins==3])
nins4<-count(Data.na.bl$trt[Data.na.bl$ins==4])
nins5<-count(Data.na.bl$trt[Data.na.bl$ins==5])
nins6<-count(Data.na.bl$trt[Data.na.bl$ins==6])
nbl<-rbind(nins3, nins4, nins5, nins6)
nblvec <- nbl$freq

```

Boxplot Body Length
```{r}

par(mfrow=c(1,1),lwd=1.5)
Data.na <-  Data[complete.cases(Data[ , 8]),]
N<-c("n=",nblvec,"","")
yrange <- range(Data.na$bl)
wid=11.5
boxplot(bl~trt*ins,data=Data.na,ylab="Length (mm)",outpch=NA,  main="Body Length",
        varwidth=F, xlim=c(.5,wid),ylim=yrange,xaxt="n",col = c("palegreen4","steelblue","tomato"))
#text(.9, 9.8, paste("T-Test
#                    GF3-GT3 p=", round(bins3$p.value, 2), sep=""), cex=.7)
#text(.9, 9.4, paste("GF4-GT4 p=", round(bins4$p.value, 2), sep=""), cex=.7)
#text(.9, 9.1, paste("GF5-GT5 p=", round(bins5$p.value, 2), sep=""), cex=.7)
stripchart(bl~trt*ins, data = Data.na[Data.na$trt=="1",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="palegreen4", 
           add = TRUE)
stripchart(bl~trt*ins, data = Data.na[Data.na$trt=="2",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE)             
stripchart(bl~trt*ins, data = Data.na[Data.na$trt=="3",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato",  
           add = TRUE)

axis(1, at=seq(3.5,wid, by=3), labels = FALSE)
text(y=5.4,x= seq(2,wid, by=3), par("usr")[3] - 0.2, labels = c("Third", "Fourth", "Fifth", "Sixth"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
legend("topleft", inset=.05, c( "Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=1)
title(xlab="Instar", line=1.5, cex.lab=1)
text(y=2.5,x= seq(0,wid, by=1), paste(labels=N,sep=""), srt = 0, xpd = TRUE, cex=1, font=1)

```


Whole Gut Anova
```{r}

Data.na.wg <-  Data[complete.cases(Data[ , 9]),]


fitwg3<- aov(wg ~ Trt, data = Data.na.wg[Data.na.wg$ins=="3",])
fitwg4<- aov(wg ~ Trt, data = Data.na.wg[Data.na.wg$ins=="4",])
fitwg5<- aov(wg ~ Trt, data = Data.na.wg[Data.na.wg$ins=="5",])

summary(fitwg3)
summary(fitwg4)
summary(fitwg5)


fitwgtk3<-TukeyHSD(fitwg3, conf.level=.99);
fitwgtk4<-TukeyHSD(fitwg4, conf.level=.99);
fitwgtk5<-TukeyHSD(fitwg5, conf.level=.99);

fitwgtk3
fitwgtk4
fitwgtk5


```
Whole gut Kruskal/Dunn 4th instar
```{r}

kruskal.test(wg~ trt, data = Data[Data$ins==4,]) 

attach(Data[Data$ins==4,])
dunn.test(wg,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==4,])
```

Whole gut Kruskal/Dunn 5th instar
```{r}

kruskal.test(wg~ trt, data = Data[Data$ins==5,]) 

attach(Data[Data$ins==5,])
dunn.test(wg,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==5,])
```
instar 6 pairwise
```{r}
wg6<-ins6[complete.cases(ins6[ , 9]),]
wg6$trt<-droplevels(wg6$trt)
wg6$ins<-droplevels(wg6$ins)
wg6w<-wilcox.test(wg~trt, data = wg6)
wg6w
```


```{r}
Data.na.wg <-  Data[complete.cases(Data[ , 9]),]
nins3<-count(Data.na.wg$trt[Data.na.wg$ins==3])
nins4<-count(Data.na.wg$trt[Data.na.wg$ins==4])
nins5<-count(Data.na.wg$trt[Data.na.wg$ins==5])
nins6<-count(Data.na.wg$trt[Data.na.wg$ins==6])
nwg<-rbind(nins3, nins4, nins5, nins6)
nwgvec <- nwg$freq

```

Whole gut Boxplot
```{r}

Data.na.wg <-  Data[complete.cases(Data[ , 9]),]
N<-c("n=",nwgvec,"","")
par(mfrow=c(1,1),lwd=1.5)
yrange <- range(Data.na.wg$wg)
wid=11.5
boxplot(wg~trt*ins,data=Data.na.wg,ylab="Length (mm)", outpch=NA, main="Whole Gut Length",
        varwidth=F,ylim=yrange, xlim=c(.5,wid),xaxt="n",col = c("palegreen4","steelblue","tomato"))
#legend("topleft", inset=.05, c( "Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=.6)
stripchart(wg~trt*ins, data = Data.na.wg[Data.na.wg$trt=="1",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Palegreen4", 
          add = TRUE)             
stripchart(wg~trt*ins, data = Data.na.wg[Data.na.wg$trt=="2",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE)
stripchart(wg~trt*ins, data = Data.na.wg[Data.na.wg$trt=="3",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato", 
           add = TRUE)

axis(1, at=seq(3.5,wid, by=3),labels=F)
y=4
text(y=y+4,x= seq(2,wid, by=3), par("usr")[3] - 0.2, labels = c("Third", "Fourth", "Fifth","sixth"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
title(xlab="Instar", line=1.5, cex.lab=1)
text(y=y-1.5,x= seq(0,wid, by=1), paste(labels=N,sep=""), pos=1,srt = 0, xpd = TRUE, cex=1)


legend("topleft", inset=.05, c("Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=1)

```


Foregut Kruskal/Dunn
```{r}

kruskal.test(fg~ trt, data = Data[Data$ins==3,]) 

attach(Data[Data$ins==3,])
dunn.test(fg,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==3,])

fg6<-ins6[complete.cases(ins6[ , 12]),]
fg6$trt<-droplevels(fg6$trt)
fg6$ins<-droplevels(fg6$ins)
fg6w<-wilcox.test(fg~trt, data = fg6)
fg6w

```


```{r}
Data.na.fg <-  Data[complete.cases(Data[ , 13]),]
nins3<-count(Data.na.fg$trt[Data.na.fg$ins==3])
nins4<-count(Data.na.fg$trt[Data.na.fg$ins==4])
nins5<-count(Data.na.fg$trt[Data.na.fg$ins==5])
nins6<-count(Data.na.fg$trt[Data.na.fg$ins==6])
nfg<-rbind(nins3, nins4, nins5, nins6)
nfgvec <- nfg$freq

```

Foregut Boxplot
```{r}
N<-c("n=",nfgvec,"")
#N<-c("n=","10","0", "3",  "19",  "9",  "22", "21",  "25", "29", "9",  "13", "")
Data.na.fg <-  Data[complete.cases(Data[ , 13]),]

par(mfrow=c(1,1),lwd=1.5)
yrange <- range(Data.na.fg$fg)
wid=11.5
boxplot(fg~trt*ins,data=Data.na.fg,ylab="Length (mm)", outpch=NA, main="Foregut Length",
        varwidth=F,ylim=yrange, xlim=c(.5,wid),xaxt="n",col = c("palegreen4","steelblue","tomato"))
#legend("topleft", inset=.05, c( "Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=.6)
stripchart(fg~trt*ins, data = Data.na.fg[Data.na.fg$trt=="1",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Palegreen4", 
          add = TRUE)             
stripchart(fg~trt*ins, data = Data.na.fg[Data.na.fg$trt=="2",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE)
stripchart(fg~trt*ins, data = Data.na.fg[Data.na.fg$trt=="3",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato", 
           add = TRUE)

axis(1, at=seq(3.5,wid, by=3),labels=F)
y=2
text(y=y,x= seq(2,wid, by=3), par("usr")[3] - 0.2, labels = c("Third", "Fourth", "Fifth","sixth"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
title(xlab="Instar", line=1.5, cex.lab=1)
text(y=y-1.5,x= seq(0,wid, by=1), paste(labels=N,sep=""), pos=1,srt = 0, xpd = TRUE, cex=1)


legend("topleft", inset=.05, c("Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=1)

```


Midgut Anova
```{r}
Data.na.mg <-  Data[complete.cases(Data[ , 11]),]

fitmg3<- aov(mg ~ Trt, data = Data[Data$ins=="3",])
fitmg4<- aov(mg ~ Trt, data = Data[Data$ins=="4",])
fitmg5<- aov(mg ~ Trt, data = Data[Data$ins=="5",])
summary(fitmg3)
summary(fitmg4)
summary(fitmg5)

fitmgtk3<-TukeyHSD(fitmg3, conf.level=.99);
fitmgtk4<-TukeyHSD(fitmg4, conf.level=.99);
fitmgtk5<-TukeyHSD(fitmg5, conf.level=.99);
fitmgtk3
fitmgtk4
fitmgtk5
```

Midgut Kruskal/Dunn 4th instar
```{r}

kruskal.test(mg~ trt, data = Data[Data$ins==5,]) 

attach(Data[Data$ins==5,])
dunn.test(mg,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==5,])
```

Midgut Kruskal/Dunn 5th instar
```{r}

kruskal.test(mg~ trt, data = Data[Data$ins==5,]) 

attach(Data[Data$ins==5,])
dunn.test(mg,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==5,])
```

insar 6 pairwise
```{r}
mg6<-ins6[complete.cases(ins6[ , 11]),]
mg6$trt<-droplevels(mg6$trt)
mg6$ins<-droplevels(mg6$ins)
mg6w<-wilcox.test(mg~trt, data = mg6)
mg6w
```

```{r}
Data.na.mg <-  Data[complete.cases(Data[ , 11]),]
nins3<-count(Data.na.mg$trt[Data.na.mg$ins==3])
nins4<-count(Data.na.mg$trt[Data.na.mg$ins==4])
nins5<-count(Data.na.mg$trt[Data.na.mg$ins==5])
nins6<-count(Data.na.mg$trt[Data.na.mg$ins==6])
nmg<-rbind(nins3, nins4, nins5, nins6)
nmgvec <- nmg$freq

```

Midgut Boxplot
```{r}
Data.na.mg <-  Data[complete.cases(Data[ , 11]),]
N<-c("n=",nmgvec,"","")

col <- c(brewer.pal(3,"Set2"))
yrange <- range(Data.na.mg$mg)
wid=11.5

boxplot(mg~trt*ins,data=Data.na.mg,ylab="Length (mm)",main="Midgut Length",outpch=NA,ylim=yrange, xlim=c(.5,wid),xaxt="n", col = c("palegreen4","steelblue","tomato"))
stripchart(mg~trt*ins, data = Data.na.mg[Data.na.mg$trt=="1",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="palegreen4", 
           add = TRUE)
stripchart(mg~trt*ins, data = Data.na.mg[Data.na.mg$trt=="2",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE)             
stripchart(mg~trt*ins, data = Data.na.mg[Data.na.mg$trt=="3",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato", 
          add = TRUE)

axis(1, at=seq(3.5,wid, by=3),labels=F)
y=0
text(y=y+2,x= seq(2,wid, by=3), par("usr")[3] - 0.2, labels = c("Third", "Fourth", "Fifth" , "Sixth"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
title(xlab="Instar", line=1.5, cex.lab=1)
text(y=y+.6,x= seq(0,wid, by=1), paste(labels=N,sep=""), pos=1,srt = 0, xpd = TRUE, cex=1)

legend("topleft", inset=.05, c("Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=1)

```

Hindgut Anova
```{r}
Data.na.hg <-  Data[complete.cases(Data[ , 10]),]
fithg3<- aov(hg ~ Trt, data = Data[Data$ins=="3",])
fithg4<- aov(hg ~ Trt, data = Data[Data$ins=="4",])
fithg5<- aov(hg ~ Trt, data = Data[Data$ins=="5",])
summary(fithg3)
summary(fithg4)
summary(fithg5)

fithgtk3<-TukeyHSD(fithg3, conf.level=.99);
fithgtk4<-TukeyHSD(fithg4, conf.level=.99);
fithgtk5<-TukeyHSD(fithg5, conf.level=.99);
fithgtk3
fithgtk4
fithgtk5
```

Hindgut Kruskal/Dunn 4th instar
```{r}

kruskal.test(hg~ trt, data = Data[Data$ins==4,]) 

attach(Data[Data$ins==4,])
dunn.test(hg,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==4,])
```

Hindgut Kruskal/Dunn 5th instar
```{r}

kruskal.test(hg~ trt, data = Data[Data$ins==5,]) 

attach(Data[Data$ins==5,])
dunn.test(hg,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==5,])
```

instar 6 pairwise
```{r}
hg6<-ins6[complete.cases(ins6[ , 10]),]
hg6$trt<-droplevels(hg6$trt)
hg6$ins<-droplevels(hg6$ins)
hg6w<-wilcox.test(hg~trt, data = hg6)
hg6w
```

```{r}
Data.na.hg <-  Data[complete.cases(Data[ , 10]),]
nins3<-count(Data.na.hg$trt[Data.na.hg$ins==3])
nins4<-count(Data.na.hg$trt[Data.na.hg$ins==4])
nins5<-count(Data.na.hg$trt[Data.na.hg$ins==5])
nins6<-count(Data.na.hg$trt[Data.na.hg$ins==6])
nhg<-rbind(nins3, nins4, nins5, nins6)
nhgvec <- nhg$freq

```

Hindgut Boxplot
```{r}

par(mfrow=c(1,1),lwd=1.5)
N<-c("n=",nhgvec,"","")
wid=11.5
yrange <- range(Data.na.hg$hg)
boxplot(hg~trt*ins,data=Data.na.hg,ylab="Length (mm)",outpch=NA, main="Hindgut Length",varwidth=F,xaxt="n", col =c("palegreen4","steelblue","tomato"),ylim=yrange,xlim=c(.5,wid))
stripchart(hg~trt*ins, data = Data.na.hg[Data.na.hg$trt=="1",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="palegreen4", 
           add = TRUE)
stripchart(hg~trt*ins, data = Data.na.hg[Data.na.hg$trt=="2",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE)             
stripchart(hg~trt*ins, data = Data.na.hg[Data.na.hg$trt=="3",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato", 
           add = TRUE)

#stripchart(hg~trt, data = Data,   
#           vertical = TRUE, method = "jitter",    
#           pch = 21, col = "black", bg ="red", 
#           add = TRUE)
wid=11.5
axis(1, at=seq(3.5,wid, by=3),labels=F)
y=0

text(y=y+1.5,x= seq(2,wid, by=3), par("usr")[3] - 0.2, labels = c("Third", "Fourth", "Fifth" , "Sixth"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
title(xlab="Instar", line=1.5, cex.lab=1)
text(y=y,x= seq(0,wid, by=1), paste(labels=N,sep=""), pos=1,srt = 0, xpd = TRUE, cex=1)



legend("topleft", inset=.05, c("Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=1)

```

Hindgut Stats by trt
```{r}
fithgt<- aov(hg ~ Trt, data = Data)

summary(fithgt)



fithgtkt<-TukeyHSD(fithgt, conf.level=.99);
fithgtkt

```

```{r}
Data.na.hg <-  Data[complete.cases(Data[ , 10]),]
nins3<-count(Data.na.hg$trt[Data.na.hg$trt==1])
nins4<-count(Data.na.hg$trt[Data.na.hg$trt==2])
nins5<-count(Data.na.hg$trt[Data.na.hg$trt==3])
nhg<-rbind(nins3, nins4, nins5)
nhgvec2 <- nhg$freq

```


Hindgut Boxplot trt
```{r}


par(mfrow=c(1,1))
N<-c("n=",nhgvec2)
Data.na.hg <-  Data[complete.cases(Data[ , 10]),]
yrange <- range(Data.na.hg$hg)
wid=3.5

plot(hg~trt,data=Data.na.hg,ylab="Width (mm)",outpch=NA, main="Hindgut Length by Treatment", xlim=c(.5,wid),ylim=yrange,xaxt="n",boxwex=.5,col = c("palegreen4","steelblue","tomato"))

stripchart(hg~trt, data = Data[Data$trt=="1",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="palegreen4", 
           add = TRUE)
stripchart(hg~trt, data = Data[Data$trt=="2",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE)             
stripchart(hg~trt, data = Data[Data$trt=="3",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato", 
           add = TRUE)

y=1.7
axis(1, at=seq(.5,wid, by=1), labels = FALSE)
text(y=y,x= seq(0,wid, by=1), par("usr")[3] - 0.2, labels = c("WT", "GT", "GF"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
#legend("topleft", inset=.05, c( "Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=1)
title(xlab="Treatment", line=1.5, cex.lab=1)
text(y=y-2.3,x= seq(0,wid, by=1), paste(labels=N,sep=""), srt = 0, xpd = TRUE, cex=1, font=1)

```



Body Mass Kruskal/Dunn 5th instar
```{r}

kruskal.test(bmass~ trt, data = Data[Data$ins==5,]) 

attach(Data[Data$ins==5,])
dunn.test(bmass,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==5,])
```
instar 6 pairwise
```{r}
bm6<-ins6[complete.cases(ins6[ , 12]),]
bm6$trt<-droplevels(bm6$trt)
bm6$ins<-droplevels(bm6$ins)
bm6w<-wilcox.test(bmass~trt, data = bm6)
bm6w
```

```{r}
Data.na.bmass <-  Data[complete.cases(Data[ , 12]),]
nins3<-count(Data.na.bmass$trt[Data.na.bmass$ins==3])
nins4<-count(Data.na.bmass$trt[Data.na.bmass$ins==4])
nins5<-count(Data.na.bmass$trt[Data.na.bmass$ins==5])
nins6<-count(Data.na.bmass$trt[Data.na.bmass$ins==6])
nbmass<-rbind(nins3, nins4, nins5, nins6)
nbmassvec <- nbmass$freq

```

Body Mass Boxplot
```{r}

par(mfrow=c(1,1),lwd=1.5)
N<-c("n=",nbmassvec,"","")
N<-c("n=", "10","0","0", "18", "9", "14","23", "11", "9", "9", "2", "", "")#update this manually
wid=11.5
yrange <- range(Data.na.bmass$bmass)
boxplot(bmass~trt*ins,data=Data.na.bmass,ylab="Mass (g)",outpch=NA, main="Body Mass",varwidth=F,xaxt="n", col = c("palegreen4","steelblue","tomato"),ylim=yrange, xlim=c(.5,wid))
stripchart(bmass~trt*ins, data = Data.na.bmass[Data.na.bmass$trt=="1",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="palegreen4", 
           add = TRUE)
stripchart(bmass~trt*ins, data = Data.na.bmass[Data.na.bmass$trt=="2",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE)             
stripchart(bmass~trt*ins, data = Data.na.bmass[Data.na.bmass$trt=="3",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato", 
           add = TRUE)

#stripchart(bmass~trt, data = Data,   
#           vertical = TRUE, method = "jitter",    
#           pch = 21, col = "black", bg ="red", 
#           add = TRUE)
wid=11.5
axis(1, at=seq(3.5,wid, by=3),labels=F)
y=-.005

text(y=y+.015,x= seq(2,wid, by=3), par("usr")[3] - 0.2, labels = c("Third", "Fourth", "Fifth" , "Sixth"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
title(xlab="Instar", line=1.5, cex.lab=1)
text(y=y-.005,x= seq(0,wid, by=1), paste(labels=N,sep=""), pos=1,srt = 0, xpd = TRUE, cex=1)



legend("topleft", inset=.05, c("Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=1)

```


Gut Mass Kruskal/Dunn 5th instar
```{r}

kruskal.test(gmass~ trt, data = Data[Data$ins==4,]) 

attach(Data[Data$ins==4,])
dunn.test(gmass,Trt, method="bonferroni", list=T)
detach(Data[Data$ins==4,])
```

instar 6 pairwise
```{r}
gmass6<-ins6[complete.cases(ins6[ , 14]),]
gmass6$trt<-droplevels(gmass6$trt)
gmass6$ins<-droplevels(gmass6$ins)
gmass6w<-wilcox.test(gmass~trt, data = gmass6)
gmass6w
```

```{r}
Data.na.gmass <-  Data[complete.cases(Data[ , 14]),]
nins3<-count(Data.na.gmass$trt[Data.na.gmass$ins==3])
nins4<-count(Data.na.gmass$trt[Data.na.gmass$ins==4])
nins5<-count(Data.na.gmass$trt[Data.na.gmass$ins==5])
nins6<-count(Data.na.gmass$trt[Data.na.gmass$ins==6])
ngmass<-rbind(nins3, nins4, nins5, nins6)
ngmassvec <- ngmass$freq

```

Gut Mass Boxplot
```{r}

N<-c("","n=","",ngmassvec,"")
N<-c( "n=",  "10","0","0", "20",  "9",  "14", "23",  "12", "9",  "9",  "2",  "" )#update this manually
par(mfrow=c(1,1),lwd=1.5)
wid=11.5

yrange <- range(Data.na.gmass$gmass)
boxplot(gmass~trt*ins,data=Data.na.gmass,ylab="Mass (g)",outpch=NA, main="Gut Mass ",varwidth=F,xaxt="n", col = c("palegreen4","steelblue","tomato"),ylim=yrange, xlim=c(.5,wid))
stripchart(gmass~trt*ins, data = Data.na.gmass[Data.na.gmass$trt=="1",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="palegreen4", 
           add = TRUE)
stripchart(gmass~trt*ins, data = Data.na.gmass[Data.na.gmass$trt=="2",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="Steelblue", 
           add = TRUE)             
stripchart(gmass~trt*ins, data = Data.na.gmass[Data.na.gmass$trt=="3",],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="tomato", 
           add = TRUE)

#stripchart(gmass~trt, data = Data,   
#           vertical = TRUE, method = "jitter",    
#           pch = 21, col = "black", bg ="red", 
#           add = TRUE)
wid=11.5
axis(1, at=seq(3.5,wid, by=3),labels=F)
y=0

text(y=y,x= seq(2,wid, by=3), par("usr")[3] - 0.2, labels = c("Third", "Fourth", "Fifth" , "Sixth"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
title(xlab="Instar", line=1.5, cex.lab=1)
text(y=y-.004,x= seq(0,wid, by=1), paste(labels=N,sep=""), pos=1,srt = 0, xpd = TRUE, cex=1)



legend("topleft", inset=.05, c("Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=1)

```


```{r}
par(mfrow=c(1,1),lwd=1.5)
wid=4.5
Data.na <-  Data[complete.cases(Data[ , 7]),]
yrange <- range(Data.na.bw$bw)
boxplot(bw~ins,data=Data.na.bw[Data.na.bw$trt==1,],ylab="Width (mm)",outpch=NA, main="Body Width vs Instar",varwidth=F,xaxt="n", col = c("red3"),ylim=yrange)
stripchart(bw~none, data = Data.na.bw[Data.na.bw$trt==1,],   
           vertical = TRUE, method = "jitter",    
           pch = 21, col = "black", bg ="red", 
           add = TRUE)
y=2
axis(1, at=seq(.5,wid, by=1), labels = FALSE)
text(y=y,x= seq(0,wid, by=1), par("usr")[3] - 0.2, labels = c("Third", "Fourth", "Fifth" , "Sixth"), srt = 0, pos = 1, xpd = TRUE, cex=.9)
#legend("topleft", inset=.05, c( "Wildtype","Germ Typical","Germ Free"), fill=c("palegreen4","steelblue","tomato"),horiz=F,cex=1)
title(xlab="Instar", line=1.5, cex.lab=1)
text(y=y-2.3,x= seq(0,wid, by=1), paste(labels=N,sep=""), srt = 0, xpd = TRUE, cex=1, font=2)
```