76 lines
3 KiB
R
76 lines
3 KiB
R
require("ggplot2")
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devtools::load_all("R/")
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## Preparing data for analysis
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interaction_data <- read.table(file = "real_data/data/interaction-data.txt", sep = "\t", header = TRUE)
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insect_orders <- unique(interaction_data$insectorder)
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plant_family <- unique(interaction_data$plantfamily)
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# All results
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iid_clustering <- readRDS("real_data/data/dore_collection_clustering_nb_run1_iid_123networks_24-05-23-21:40:42.Rds")
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iid_best_partition <- extract_best_bipartite_partition(iid_clustering)
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iid_unlist <- unlist(iid_best_partition)
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rho_clustering <- readRDS("real_data/data/dore_collection_clustering_nb_run1_rho_123networks_25-05-23-13:58:30.Rds")
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rho_best_partition <- extract_best_bipartite_partition(rho_clustering)
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rho_unlist <- unlist(rho_best_partition)
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pi_clustering <- readRDS("real_data/data/dore_collection_clustering_nb_run1_pi_123networks_25-05-23-17:31:25.Rds")
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pi_best_partition <- extract_best_bipartite_partition(pi_clustering)
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pi_unlist <- unlist(pi_best_partition)
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pirho_clustering <- readRDS("real_data/data/dore_collection_clustering_nb_run1_pirho_123networks_26-05-23-19:22:55.Rds")
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pirho_best_partition <- extract_best_bipartite_partition(pirho_clustering)
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pirho_unlist <- unlist(pirho_best_partition)
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### Matching taxonomy
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taxonomy_in_clusters <- function(unlisted_model) {
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lapply(seq_len(length(unlisted_model)), function(col_idx) {
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# Per collection
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# Empty init
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insect_count <- t(sapply(insect_orders, function(order) {
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out_count <- rep(0, unlisted_model[[col_idx]]$Q[2])
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out_count
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}))
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plant_count <- t(sapply(plant_family, function(order) {
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out_count <- rep(0, unlisted_model[[col_idx]]$Q[1])
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out_count
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}))
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for (m in seq.int(unlisted_model[[col_idx]]$M)) {
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#### Insect
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insect_names <- names(unlisted_model[[col_idx]]$Z[[1]][[2]])
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insect_count <- insect_count + t(sapply(insect_orders, function(order) {
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out_count <- rep(0, unlisted_model[[col_idx]]$Q[2])
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names(out_count) <- seq.int(unlisted_model[[col_idx]]$Q[2])
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insect_count <- table(unlisted_model[[col_idx]]$Z[[m]][[2]][grep(order, insect_names)])
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out_count[names(insect_count)] <- insect_count
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out_count
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}))
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#### Plants
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plant_names <- names(unlisted_model[[col_idx]]$Z[[1]][[1]])
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plant_count <- t(sapply(plant_family, function(order) {
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out_count <- rep(0, unlisted_model[[col_idx]]$Q[1])
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names(out_count) <- seq.int(unlisted_model[[col_idx]]$Q[1])
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plant_count <- table(unlisted_model[[col_idx]]$Z[[m]][[1]][grep(order, plant_names)])
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out_count[names(plant_count)] <- plant_count
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out_count
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}))
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}
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return(list(insects = insect_count, plants = plant_count))
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})
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}
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taxonomy_remove_empty <- function(taxonomy_collections_list) {
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lapply(taxonomy_collections_list, function(collection) {
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list(
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insects = collection$insects[which(rowSums(collection$insects != 0) > 0), ],
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plants = collection$plants[which(rowSums(collection$plants != 0) > 0), ]
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)
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})
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}
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