Figures

library(tidyverse)
library(ggtext)
library(cowplot)
library(png)
library(grid)

Set up paths

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

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)

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

KEGG_30 <- readRDS(file.path(anvio_folder, "metabolic_analysis/NovCor_KEEG_Figure.rds")) 

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)