effector.Rmd

---
title: "PTR-60-75 effectors"
author: "Paula Moolhuijzen"
date: "Date: `r format(Sys.time(), '%d %B, %Y')`"
output: html_document
---

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

```

libraries loaded

```{r, echo=FALSE, message=FALSE, include=FALSE}
getwd()
setwd(getwd())
print(getwd())
```

## R load libraries

```{r}
library(ggplot2)
library(dplyr)
library(ggrepel)
library(ggpubr)
```



### read in effectors data

```{r}
tbl <- read.table("effector.txt", sep="\t", header = FALSE, stringsAsFactors=TRUE)
#str(tbl)
```

## set headers

```{r}
names(tbl) <-c(V1="Group", V2="Gene", V3="Length", V4="Score")
#head(tbl)
```

## Compare means effector length

```{r}
compare_means(Length ~ Group, data = tbl)
```

## boxplot effector lengths

```{r}
p1 <- ggplot(tbl, aes(x=Group, y=Length, fill=Group)) +
  geom_boxplot()

p1
```

## boxplot effector scores

```{r}
p2 <- ggplot(tbl, aes(x=Group, y=Score, fill=Group)) +
  geom_boxplot() 
p2
```


## Compare means effector scores

```{r}
compare_means(Score ~ Group, data = tbl)
```

## boxplot effector A) length and B) score
```{r}
pdf(file="effector-boxplots.pdf")

ggarrange(p1, p2, labels = c("A", "B"),
          ncol = 2, nrow = 1)

dev.off()
```

```{r}
sessionInfo()
```