plot_world.Rmd

---
title: "Plot_world isolates"
author: "Paula Moolhuijzen"
date: '`r format(Sys.time(), "%d %B, %Y")`'
output: html_document
---

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

Yes
```{r}
getwd()
setwd(getwd())
print(getwd())
```

## libraries

```{r, echo=FALSE}
library(plotly)
library(dplyr)
library(ggplot2)
```


```{r, echo=FALSE}
iso <- read.table("isolates.txt", sep="\t", header = TRUE)
world <- map_data("world")

worldmap <-ggplot() +
  geom_map(
    data = world, map = world,
    aes(long, lat, map_id = region),
    color = "gray", fill = "white", size = 0.1
  ) +
  theme_void() +
  theme(legend.position = "none")

head(world)

```

```{r, echo=FALSE}
world$isolates[world$region == 'UK'] <- 1
world$isolates[world$region == 'Germany'] <- 3
world$isolates[world$region == 'Denmark'] <- 3
world$isolates[world$region == 'Tunisia'] <- 2
world$isolates[world$region == 'Algeria'] <- 2
world$isolates[world$region == 'Brazil'] <- 1
world$isolates[world$region == 'USA'] <- 6
world$isolates[world$region == 'Canada'] <- 2
world$isolates[world$region == 'Australia'] <- 6
```


```{r, echo=FALSE}
p <- ggplot()
p <- p + geom_polygon( data=world, 
                       aes(x=long, y=lat, group=group, fill = isolates),
                       color="white", size = 0.1) +
  theme_void() 

p + labs(fill = "No. isolates") +
  theme(legend.position = "bottom", legend.title = element_text(color = "black", size = 12))

p +theme(legend.position = "bottom")

```

```{r}
pdf(file="world_map.pdf", width=10, height=5) 
p + labs(fill = "No. isolates") +
  theme(legend.position = "bottom", legend.title = element_text(color = "black", size = 12))
dev.off()
```



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