---
title: "R Notebook"
output: html_notebook
---
This is an [R Markdown](http://rmarkdown.rstudio.com) Notebook. When you execute code within the notebook, the results appear beneath the code.
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```{r}
plot(cars)
library("readr")
IsosWA3 <- read.csv("~/Dropbox/Sgro Lab/PEOPLE/Avi/Chapter 3/Selected_lines_exps/Female_adult_wing_area_final.csv")
head (IsosWA3)
```
```{r}
require(dplyr)
library(lme4)
library(emmeans)
library (ggplot2)
IsosWA3$Line <- as.factor(IsosWA3$Line)
```
```{r}
IsosWA.lm3 <- lmer (Wing_area ~ 1+ Temp * Conc + (1|Replicate) + (1|Line) , data = IsosWA3)
summary (IsosWA.lm3)
car::Anova(IsosWA.lm3)
IsosWA.lm4 <- lmer (Wing_area ~ Temp * Diet *Line + (1|Replicate) , data = IsosWA3)
summary (IsosWA.lm4)
car::Anova(IsosWA.lm4)
IsosWA.lm5 <- lm (Wing_area ~ Temp * Conc *Line + (1|Replicate) , data = IsosWA3)
summary (IsosWA.lm5)
car::Anova(IsosWA.lm5)
anova (IsosWA.lm5, IsosWA.lm4)
#checking for plasticity level group differences
IsosWA.lm6 <- lmer (Wing_area ~ Temp * Conc *PL + (1|Replicate) + (1|Line) , data = IsosWA3)
summary (IsosWA.lm6)
car::Anova(IsosWA.lm6)
Isos_trend <- emtrends(IsosWA.lm5, ~ Temp | Line, var = "Conc")
multcomp::cld(Isos_trend)
#line 36 differ in response of diet at the two temperature, steeper response to diet at 25 than 28
```
```{r}
PLOT3 <- ggplot(data = IsosWA3, aes(x=Conc, y=Wing_area, group=Line, colour=as.factor(PL)))+
theme_bw()+
#theme(panel.grid=element_blank(),axis.title.x=element_text(size=16), axis.title.y=element_text(size=16), axis.text.y=element_text(size=16), axis.text.x=element_text(size=12), legend.background = element_rect(), legend.key = element_rect(colour = "white"), legend.text=element_text(face="italic", size=12))+
#scale_colour_hue(name = "line_number") +
#theme(legend.title=element_blank())+ expand_limits(x=0.1) +
#geom_point(size=2.5) +
#geom_line(data=IsosWing, aes(x=Diet_dilution, y=wing_area, group=Line),stat="smooth",method = "loess",size = 1,alpha = 0.1)+
geom_smooth( method="lm", se=FALSE)+
#geom_smooth (method="lm",formula = y ~ poly(x,2,raw=TRUE), se = FALSE, aes (fill = as.factor (Line)))+
scale_x_continuous( breaks = c (12.5, 100))+ scale_y_continuous (limits= c(0.65,1.25), breaks = seq (0.65, 1.25, 0.1)) + geom_point (alpha=0.3)+ geom_jitter() +
#scale_x_continuous( breaks = seq (12.5, 25, 100))+
#guides (fill=FALSE) +
#geom_smooth for black line mean
facet_grid(~ Temp)+
xlab("Diet_dilution")+ylab("Wing area ")+
geom_blank()
PLOT3
pdf("./WingAreaSelectedLines_response_PLgroup.pdf", useDingbats=FALSE)
grid.arrange(PLOT3)
dev.off()
```
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