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()