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Enlevement du chargement du fichier de données

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Louis Lacoste 2024-05-07 18:08:54 +02:00
parent f700bd8bbb
commit 9da1a25735
1 changed files with 33 additions and 39 deletions
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72
code/applications/dore/01_dore_clusterize.R
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@ -39,51 +39,45 @@ collection_data <- file.path(
"dore-matrices.Rds"
)
if (!file.exists(collection_data)) {
interaction_data <- read.table(file = file.path(base_data_folder, "interaction-data.txt"), sep = "\t", header = TRUE)
interaction_data <- read.table(file = file.path(base_data_folder, "interaction-data.txt"), sep = "\t", header = TRUE)
seq_ids_network_aggreg <- unique(interaction_data$id_network_aggreg)
names_aggreg_networks <- sapply(
seq_ids_network_aggreg,
function(id) {
paste0(
unique(interaction_data[which(interaction_data$id_network_aggreg == id), ]$web),
collapse = "+"
)
}
)
# Computation of incidence matrices
incidence_matrices <- lapply(
seq_ids_network_aggreg,
function(m) {
current_interaction_data <- interaction_data[which(interaction_data$id_network_aggreg == m), ] %>%
mutate(
plantaggreg = paste(plantorder,
plantfamily, plantgenus, plantspecies,
sep = "-"
),
insectaggreg = paste(insectorder,
insectfamily, insectgenus, insectspecies,
sep = "-"
)
seq_ids_network_aggreg <- unique(interaction_data$id_network_aggreg)
names_aggreg_networks <- sapply(
seq_ids_network_aggreg,
function(id) {
paste0(
unique(interaction_data[which(interaction_data$id_network_aggreg == id), ]$web),
collapse = "+"
)
}
)
# Computation of incidence matrices
incidence_matrices <- lapply(
seq_ids_network_aggreg,
function(m) {
current_interaction_data <- interaction_data[which(interaction_data$id_network_aggreg == m), ] %>%
mutate(
plantaggreg = paste(plantorder,
plantfamily, plantgenus, plantspecies,
sep = "-"
),
insectaggreg = paste(insectorder,
insectfamily, insectgenus, insectspecies,
sep = "-"
)
current_interaction_data <- table(current_interaction_data$plantaggreg, current_interaction_data$insectaggreg)
current_incidence_matrix <- matrix(current_interaction_data,
ncol = ncol(current_interaction_data), dimnames = dimnames(current_interaction_data)
)
current_interaction_data <- table(current_interaction_data$plantaggreg, current_interaction_data$insectaggreg)
current_incidence_matrix[which(current_incidence_matrix > 0)] <- 1
return(current_incidence_matrix)
}
)
current_incidence_matrix <- matrix(current_interaction_data,
ncol = ncol(current_interaction_data), dimnames = dimnames(current_interaction_data)
)
names(incidence_matrices) <- names_aggreg_networks
current_incidence_matrix[which(current_incidence_matrix > 0)] <- 1
return(current_incidence_matrix)
}
)
saveRDS(incidence_matrices, file = collection_data)
}
incidence_matrices <- readRDS(collection_data)
names(incidence_matrices) <- names_aggreg_networks
start_time <- format(Sys.time(), "%d-%m-%y_%H-%M-%S")