37 lines
1.3 KiB
R
37 lines
1.3 KiB
R
if ("MicroBioMap" %in% rownames(installed.packages()) == FALSE) {
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cat("MicroBioMap package not found. Installing...\n")
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if (!requireNamespace("BiocManager", quietly = TRUE)) {
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install.packages("BiocManager")
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}
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BiocManager::install("blekhmanlab/MicroBioMap")
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}
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library(MicroBioMap)
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library(countrycode)
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library(igraph)
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library(here)
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library(readr)
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setClassUnion("ExpData", c("matrix", "SummarizedExperiment"))
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cpd <- getCompendium(version = "1.0.1")
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colData(cpd)$country <- countrycode(colData(cpd)$iso, "iso2c", "country.name")
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projects <- unique(colData(cpd)$project)
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save_folder <- here("data")
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if (!dir.exists(save_folder)) {
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dir.create(save_folder)
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}
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for (project in projects) {
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cat("Processing project:", project, "\n")
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# Filter the compendium for the current project
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project_data <- cpd[, colData(cpd)$project == project]
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matrix_data <- counts(project_data)
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# Create a graph from the matrix data
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g <- graph_from_biadjacency_matrix(matrix_data)
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edge_list <- as_edgelist(g) |> as.data.frame()
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colnames(edge_list) <- c("source", "target")
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write_csv(edge_list, file = here(save_folder, paste0(project, "_edge_list.csv.gz")))
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supinfo_df <- as.data.frame(colData(project_data))
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write_csv(supinfo_df, file = here(save_folder, paste0(project, "_supinfo.csv.gz")))
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}
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