test: add original code to base pkg off of

.Rbuildignore

@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
+^R/TEMP_original_fxns\.R$

.gitignore

@@ -38,3 +38,4 @@ inst/doc
 .Rproj.user/
 data-raw/*.rds
 .Rhistory
+.Rproj.user

R/TEMP_original_fxns.R

@@ -0,0 +1,130 @@
+###########################################
+## Extracting Results from a HotNet2 Run ##
+###########################################
+
+library(igraph)
+library(tidygraph)
+library(RColorBrewer)
+library(scales)
+library(reshape)
+library(pryr)
+library(data.table)
+library(plyr)
+library(magrittr)
+library(tidyverse)
+
+#### ---- Subroutines ---- ####
+
+# gets the k for a given delta
+get_k_for_delta <- function(d) {
+ sig_tib <- read_tsv(paste0(d, "/significance.txt"),
+ progress = FALSE, col_types = cols())
+ colnames(sig_tib) <- c("size", "expected", "actual", "pval")
+ return(sig_tib)
+}
+
+# finds the optimal delta value
+get_best_delta <- function(dt) {
+ d_best <- dt %>%
+ group_by(delta) %>%
+ summarise(sig_ks = sum(pval < 0.05)) %>%
+ ungroup() %>%
+ filter(sig_ks > 0) %>%
+ arrange(desc(sig_ks), delta) %>%
+ slice(1) %>%
+ pull(delta)
+ if (length(d_best) > 0) {
+ return(d_best)
+ } else {
+ # if no significant deltas
+ return(NA)
+ }
+}
+
+# returns the best k for a delta
+get_best_k <- function(dt, d) {
+ k_best <- dt %>%
+ filter(delta == d) %>%
+ filter(pval < 0.05) %>%
+ pull(size)
+ return(min(k_best))
+}
+
+uuid_list <- c()
+list_to_full_graph <- function(x) {
+ gr_uuid <- sample(1E8, 1)
+ while (gr_uuid %in% uuid_list) gr_uuid <- sample(1E8, 1)
+ uuid_list <- c(uuid_list, gr_uuid)
+ gr <- make_full_graph(length(x)) %>%
+ as_tbl_graph(directed = FALSE) %>%
+ mutate(name = unlist(x),
+ uuid = gr_uuid)
+ return(gr)
+}
+
+# recursively bind a list of graphs
+recursively_bind_graphs <- function(gr_list) {
+ if (length(gr_list) == 1) {
+ # base case
+ return(gr_list[[1]])
+ } else {
+ # recurse
+ GR <- bind_graphs(gr_list[[1]], recursively_bind_graphs(gr_list[-1]))
+ }
+ return(GR)
+}
+
+# returns the components of the HotNet results
+get_components <- function(dir, min_size) {
+ comp_file <- paste0(dir, "/components.txt")
+ comps <- readLines(comp_file)
+ comps <- unlist(lapply(comps, str_split, pattern = "\\\t"),
+ recursive = FALSE)
+ comps_gr <- map(comps, list_to_full_graph)
+ Gr <- recursively_bind_graphs(comps_gr) %>%
+ convert(to_undirected, .clean = TRUE) %N>%
+ select(name, uuid) %E>%
+ select(from, to)
+ return(Gr)
+}
+
+#### ---- Main Function ---- ####
+
+# gets the subnet from a HotNet2 run
+# just pass in the directory where the results were posted
+get_HN2_subnetworks <- function(hn2_dir) {
+ delta_dirs <- list.files(hn2_dir,
+ pattern = "delta",
+ full.names = TRUE)
+ delta_tib <- lapply(delta_dirs, get_k_for_delta)
+ names(delta_tib) <- basename(delta_dirs)
+ delta_tib <- as_tibble(ldply(delta_tib, data.frame, .id = "delta")) %>%
+ mutate(delta = as.numeric(str_remove_all(delta, "delta\\_")))
+ d <- get_best_delta(delta_tib)
+ if (is.na(d)) {
+ cat("\nno significant subnetworks\n")
+ HNsubs <- create_empty(n = 0, directed = FALSE) %N>%
+ mutate(name = "EMPTY_NODE", uuid = "EMPTY_NODE") %>%
+ slice(0)
+ k <- Inf
+ cat("-----------------------------------\n\n")
+ } else {
+ k <- max(get_best_k(delta_tib, d), 2)
+ d_dir <- str_subset(delta_dirs, str_sub(as.character(d), 1, 11))
+ HNsubs <- get_components(d_dir, k)
+ cat("\ntrial:", basename(hn2_dir), "\n")
+ cat("number of nodes:", vcount(HNsubs), "\n")
+ cat("number of components:", count_components(HNsubs), "\n")
+ cat("-----------------------------------\n\n")
+ }
+ return(list(sample_name = basename(hn2_dir),
+ delta = d,
+ size = k,
+ subnetworks = HNsubs))
+}
+
+
+#### ---- Example ---- ####
+
+# coad_a146t_path <- "OUTPUT/COAD_results/coad_hint-coad_kras_a146t_hint_heat"
+# coad_a146t_hn2 <- get_HN2_subnetworks(coad_a146t_path)