Complentation Plot.Rmd

---
title: "Complementation Graph"
author: "Julin N Maloof"
date: "3/31/2018"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r}
library(tidyverse)
library(stringr)
data <- read_csv("tie1comp.csv") %>% 
  filter(!is.na(line_1)) %>%
  mutate(line_1=str_replace(line_1,"(^[24])","GA2ox7-\\1")) %>%
  mutate(length=ifelse(str_detect(line,"mix"),NA,length))
data
```

```{r}
unique(data$line_1)
data$line_1 <- factor(data$line_1, levels = c("tie1","GA2ox7-2","GA2ox7-4","M82"))
lm1 <- lm(length~line_1,data=data)
summary(lm1)
```

```{r}
data$line_1 <- relevel(data$line_1, ref="M82")
lm2 <- lm(length~line_1,data=data)
summary(lm2)
```


```{r}
data %>% mutate(line_1=relevel(line_1,ref="tie1")) %>%
  group_by(line_1) %>%
  summarize(mean_expression=mean(expression,na.rm=TRUE), 
            mean_length=mean(length,na.rm=TRUE),
            exp_error=sd(expression,na.rm=TRUE)/sqrt(length(na.omit(expression))),
            length_error=sd(length,na.rm=TRUE)/sqrt(length(na.omit(length)))) %>%
ggplot(aes(x=mean_expression,y=mean_length,color=line_1,shape=line_1) )+
  geom_point(size=3) +
  geom_errorbar(aes(ymax=mean_length+length_error,ymin=mean_length-length_error),width=.35) +
  geom_errorbarh(aes(xmax=mean_expression+exp_error,xmin=mean_expression-exp_error),height=1.8) +
  scale_shape_manual(values=15:18) +
  scale_color_manual(values=c("M82"="grey80","tie1"="grey20","GA2ox7-2"="grey50","GA2ox7-4"="grey50")) +
  xlab("Relative Expression Level") +
  ylab("Epicotyl Length (mm)") +
  theme_bw() +
  theme(legend.title = element_blank())
ggsave("~/Google Drive/tie paper resubmission/ComplementationFigure.pdf",height=2.75,width=4)

```