roary-plot.Rmd

---
title: "Roary.Pan-Genome_Plot"
author: "Shawn Higdon"
date: "4/7/2020"
output: html_document
---

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

## Libraries
```{r, message=FALSE}
library(tidyverse)
library(cowplot)
```

## Reformat SVG Image
```{r panels}

# read in pan-genome pie chart
pie <- ggdraw() + draw_image("./plots/roary_pie.png")

# read in pan-genome gene diversity plot
line <- ggdraw() + draw_image("./plots/conserved_vs_total_genes.png")


# read in matrix plot
pg_mat <- ggdraw() + draw_image("./plots/matrix.png")

pie
line
pg_mat
```

```{r fonts}
library(extrafont)

#font_import() # run this once

loadfonts(device = "pdf", quiet = TRUE)

```


```{r cowplot}

theme_set(theme_cowplot(font_family = "Palatino Linotype"))

# array

Fig2_top <- plot_grid(pie,
                      line,
                      ncol = 2,
                      nrow = 1,
                      align = 'h',
                      labels = c("A", "B"),
                      label_size = 42)

Fig2_top

Fig2 <- plot_grid(Fig2_top,
                  pg_mat,
                  ncol = 1,
                  nrow = 2,
                  labels = c("", "C"),
                  label_size = 42,
                  align = 'vh')


Fig2

#Fig2
ggsave("./plots/Fig2.pdf", Fig2, width = 18, height = 20, device = cairo_pdf)

```