---
execute:
eval: TRUE
message: FALSE
warning: FALSE
---
# Figures {.unnumbered}
```{r}
library(tidyverse)
library(ggtext)
library(cowplot)
library(png)
library(grid)
```
## Set up paths
```{r}
FOLDER_PATH <- Sys.getenv("DATA_PATH")
ani_folder <- file.path(FOLDER_PATH, "pyani-plus")
ggdc_folder <- file.path(FOLDER_PATH, "GGDC")
anvio_folder <- file.path(FOLDER_PATH, "anvio-9")
figures_folder <- file.path(FOLDER_PATH, "FIGURES")
if (!dir.exists(figures_folder)) {
dir.create(figures_folder)
}
```
## Figure 2
```{r}
pANI_30 <- readRDS(file.path(ani_folder, "NovCor_ANI_NovCor_30_CtuComplex.rds"))
dDDH_30 <- readRDS(file.path(ggdc_folder, "NovCor_dDDH_NovCor_30_CtuComplex.rds"))
key <- readPNG(file.path(figures_folder, "ColorKey.png"))
key <- rasterGrob(key, interpolate = TRUE)
```
```{r, fig.align="center",fig.width=12, fig.height=18}
fig2 <- plot_grid(
pANI_30, dDDH_30, key,
labels = c("A", "B", ""), rel_heights = c(1, 1, 0.05), ncol = 1
)
fig2
ggsave(plot = fig2, file.path(figures_folder, "Figure_2.png"), width = 12, height = 18)
ggsave(plot = fig2, file.path(figures_folder, "Figure_2.svg"), width = 12, height = 18)
ggsave(plot = fig2, file.path(figures_folder, "Figure_2.jpeg"), width = 12, height = 18)
```
## Figure 4
```{r}
KEGG_30 <- readRDS(file.path(anvio_folder, "metabolic_analysis/NovCor_KEEG_Figure.rds"))
```
```{r, fig.align="center",fig.width=12, fig.height=13}
fig4 <- plot_grid(
key, KEGG_30,
rel_heights = c(0.05, 1), ncol = 1
)
fig4
ggsave(plot = fig4, file.path(figures_folder, "Figure_4.png"), width = 12, height = 13)
ggsave(plot = fig4, file.path(figures_folder, "Figure_4.svg"), width = 12, height = 13)
ggsave(plot = fig4, file.path(figures_folder, "Figure_4.jpeg"), width = 12, height = 13)
```
