From 47fe4de8891277aaa2ffafec00631c66602bb58f Mon Sep 17 00:00:00 2001
From: Louis <louis.lacoste@agroparistech.fr>
Date: Mon, 13 Oct 2025 10:26:20 +0200
Subject: [PATCH] Created a script to generate nice visuals for slides

---
 generate-figures.R | 82 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 generate-figures.R

diff --git a/generate-figures.R b/generate-figures.R
new file mode 100644
index 0000000..7c6d2e2
--- /dev/null
+++ b/generate-figures.R
@@ -0,0 +1,82 @@
+source("utils.R")
+library(stringr)
+
+if (!file.exists("data/hmc-phyloseq-europe.Rds")) {
+    source("load-europe.R")
+} else {
+    cpd_phyloseq_europe <- readRDS("data/hmc-phyloseq-europe.Rds")
+}
+
+df <- otu_table(cpd_phyloseq_europe)
+colnames(df) <- paste0("$S_{", seq(1, ncol(df)), "}$")
+
+
+nr <- 6
+nc <- 6
+
+sub_df <- ellipse_table(df, nr = nr, nc = nc)
+
+taxo_df <-
+    rownames(sub_df)[-(ceiling(nr / 2) + 1)] |>
+    str_replace_all(" ", "") |>
+    strsplit("\\.") |>
+    do.call(what = "rbind") |>
+    as.data.frame()
+
+colnames(taxo_df) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus")
+
+rownames(sub_df) <- c(taxo_df[seq(1, ceiling((nr / 2))), "Genus"], rownames(sub_df)[(ceiling(nr / 2) + 1)], taxo_df[seq(ceiling((nr / 2)) + 1, nrow(taxo_df)), "Genus"])
+
+
+kable(sub_df, format = "latex", escape = FALSE, align = "c") |>
+    writeLines(con = file.path("outfiles", "otu-tabular.tex"))
+
+library(data.tree)
+library(ape)
+library(ggtree)
+library(ggplot2)
+library(dplyr)
+# Create a path string column from your hierarchy
+levels_vec <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus")
+taxo_df$pathString <- apply(
+    taxo_df[, levels_vec],
+    1,
+    function(x) paste(x, collapse = "/")
+)
+
+# Now build the tree
+taxo_tree <- as.Node(taxo_df)
+
+taxo_phylo <- as.phylo(taxo_tree)
+
+# 3. Extract node data
+p <- ggtree(taxo_phylo, layout = "rectangular")
+node_data <- p$data
+
+# 4. Build lookup table: each label → its rank
+lookup <- taxo_df %>%
+    tidyr::pivot_longer(cols = all_of(levels_vec), names_to = "rank_name", values_to = "label")
+
+# 5. Join node data with taxonomy ranks
+node_data2 <- node_data %>%
+    left_join(lookup, by = "label") %>%
+    mutate(rank_name = factor(rank_name, levels = levels_vec)) # enforce order
+
+internal_nodes <- node_data2
+
+library(ggokabeito)
+# 6. Plot with colored nodes
+(phylo_plot <- ggtree(taxo_phylo, layout = "slanted") %<+% node_data2 +
+    geom_point(aes(color = rank_name), size = 3, na.rm = TRUE) +
+    geom_text2(aes(label = label, color = rank_name),
+        hjust = 1.1, vjust = -1, size = 4, na.rm = TRUE
+    ) +
+    scale_colour_okabe_ito(name = "Taxonomic Rank", order = c(1:3, 5:7)) +
+    theme_void() +
+    theme(legend.position = "none"))
+library(tikzDevice)
+# Set up tikzDevice to use standalone document class
+options(tikzDocumentDeclaration = "\\documentclass[10pt]{standalone}")
+tikz(file = file.path("outfiles", "otu-phylo.tex"), height = 9, , width = 15, standAlone = TRUE)
+phylo_plot
+dev.off()