diff --git a/.Rbuildignore b/.Rbuildignore
index 931662b..dbea8b6 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
+^R/TEMP_original_fxns\.R$
diff --git a/.gitignore b/.gitignore
index 37e0f80..0ac65d8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -38,3 +38,4 @@ inst/doc
 .Rproj.user/
 data-raw/*.rds
 .Rhistory
+.Rproj.user
diff --git a/R/TEMP_original_fxns.R b/R/TEMP_original_fxns.R
new file mode 100644
index 0000000..c8ac5ae
--- /dev/null
+++ b/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)