## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

## ----setup--------------------------------------------------------------------
# library(unitcm)
# library(dplyr)

## ----select-formula-----------------------------------------------------------
# formulas <- search_formulas(q = "insomnia", page_size = 5)
# formulas
# 
# # Get full details for the first formula
# formula <- get_formula(formulas$order[1])
# formula$formula_name
# formula$composition

## ----get-doses----------------------------------------------------------------
# doses <- get_formula_doses(formulas$order[1])
# doses
# 
# # Extract herb names
# herb_names <- doses$herb_name
# herb_names

## ----find-herbs---------------------------------------------------------------
# herb_data <- lapply(herb_names, function(name) {
#   result <- search_herbs(q = name, page_size = 1)
#   if (nrow(result) > 0) result[1, ]
# })
# herb_data <- bind_rows(herb_data)
# herb_data

## ----get-compounds------------------------------------------------------------
# all_compounds <- lapply(herb_data$unitcm_herb_id, function(hid) {
#   comps <- get_herb_compounds(hid, all_pages = TRUE)
#   if (nrow(comps) > 0) comps$herb_id <- hid
#   comps
# })
# all_compounds <- bind_rows(all_compounds)
# 
# # Unique compounds
# unique_compounds <- distinct(all_compounds, unitcm_ingredient_id,
#                              .keep_all = TRUE)
# cat(nrow(unique_compounds), "unique compounds found\n")

## ----get-targets--------------------------------------------------------------
# # Get targets for top compounds (limit to first 10 for speed)
# top_compounds <- head(unique_compounds, 10)
# 
# all_targets <- lapply(top_compounds$unitcm_ingredient_id, function(cid) {
#   targets <- get_compound_targets(cid, method = "drugclip")
#   if (nrow(targets) > 0) targets$compound_id <- cid
#   targets
# })
# all_targets <- bind_rows(all_targets)
# cat(length(unique(all_targets$gene_symbol)), "unique targets found\n")

## ----build-network------------------------------------------------------------
# library(igraph)
# 
# # Herb-Compound edges
# hc_edges <- all_compounds |>
#   select(from = herb_id, to = unitcm_ingredient_id) |>
#   distinct()
# 
# # Compound-Target edges
# ct_edges <- all_targets |>
#   select(from = compound_id, to = gene_symbol) |>
#   distinct()
# 
# # Combine edges
# edges <- bind_rows(hc_edges, ct_edges)
# 
# # Build graph
# g <- graph_from_data_frame(edges, directed = FALSE)
# 
# # Add node type attribute
# V(g)$type <- case_when(
#   V(g)$name %in% herb_data$unitcm_herb_id ~ "herb",
#   V(g)$name %in% unique_compounds$unitcm_ingredient_id ~ "compound",
#   TRUE ~ "target"
# )
# 
# cat("Network:", vcount(g), "nodes,", ecount(g), "edges\n")

## ----plot-network, fig.width = 10, fig.height = 8-----------------------------
# library(ggraph)
# 
# ggraph(g, layout = "fr") +
#   geom_edge_link(alpha = 0.3) +
#   geom_node_point(aes(color = type, size = type)) +
#   scale_color_manual(values = c(herb = "#e74c3c", compound = "#3498db",
#                                 target = "#2ecc71")) +
#   scale_size_manual(values = c(herb = 6, compound = 3, target = 2)) +
#   geom_node_text(
#     aes(label = ifelse(type == "herb", name, "")),
#     repel = TRUE, size = 3
#   ) +
#   theme_void() +
#   labs(title = paste("H-C-T Network:", formula$formula_name))

## ----enrichment---------------------------------------------------------------
# target_genes <- unique(all_targets$gene_symbol)
# enrichment <- query_disease_enrichment(
#   target_genes,
#   p_value_cutoff = 0.05,
#   correction_method = "fdr"
# )
# head(enrichment, 10)