Pushing code that I forgot to push sooner

results/2023-0215/tutorial_extract-non-overlapping-regions.R

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+#!/bin/env Rscript
+
+#  tutorial_extract-non-overlapping-regions.R
+#  AntoniosK, me
+#  2015-0812
+
+#  - See stackoverflow.com/questions/31968890/how-to-extract-non-overlapping-ranges-of-field-region-using-r
+#  - See stackoverflow.com/questions/16957293/collapse-intersecting-regions
+
+
+#  Initialize functions -------------------------------------------------------
+`%+=%` <- function(x, y) eval.parent(substitute(x <- x + y))
+# stackoverflow.com/questions/5738831/r-plus-equals-and-plus-plus-equivalent-from-c-c-java-etc
+
+
+detect_overlap <- function(x, y) {
+    # Detect overlaps
+    # :param x: row number <numeric>
+    # :param y: range start and end columns/vectors <numeric>
+    # :return z: Boolean <0 or 1>
+    z <- ifelse(x[2] >= y[1], 1, 0)
+    return(z)
+}
+
+
+# delete_overlap <- function(x, y) {
+#     # Delete row that overlaps previous row from dataframe/tibble
+#     # :param x: dataframe/tibble
+#     # :param y: range start and end columns/vectors <numeric>
+#     # :return x: dataframe/tibble sans rows that overlapped previous row
+#     i <- 2
+#     while(i <= nrow(x)) {
+#         # i <- 2
+#         tmp <- x
+#         if(detect_overlap(tmp[i - 1, y], tmp[i, y]) == 1) {
+#             tmp[i, ] <- NA
+#             x <- tmp[complete.cases(tmp), ]
+#         } else {
+#             x <- tmp
+#             i %+=% 1
+#         }
+#     }
+# 
+#     return(x)
+# }
+
+
+#  Initialize example dataframe -----------------------------------------------
+df <- data.frame(
+    seqname = c(rep("I", 4), rep("II", 5)),
+    start = c(1, 20, 101, 220, 1, 100, 130, 300, 301),
+    end = c(100, 120, 200, 280, 50, 150, 180, 400, 350)
+)
+
+# order data based on minimum value of range (in case you don't have an order already)
+df <- df[order(df$seqname, df$start, df$end), ]
+df
+
+# region start end
+# 1       I     1 100
+# 2       I    20 120
+# 3       I   101 200
+# 4       I   220 280
+# 5      II     1  50
+# 6      II   100 150
+# 7      II   130 180
+# 8      II   300 400
+# 9      II   301 350
+
+
+#  Compares each row with the previous one, deleting rows that overlap --------
+#  Without accounting for chr/seqname ---------------------
+# i <- 2  # Set starting row
+# while(i <= nrow(df)) {
+#     # i <- 4
+#     df_tmp <- df
+#     if(overlap(df_tmp[i - 1, 2:3], df_tmp[i, 2:3]) == 1) {
+#         df_tmp[i, ] <- NA
+#         df <- df_tmp[complete.cases(df_tmp), ]
+#     } else {
+#         df <- df_tmp
+#         i %+=% 1
+#     }
+# }
+# df
+
+#  With accounting for chr/seqname ------------------------
+out <- plyr::ddply(
+    df,
+    "seqname",
+    function(x) {
+        i <- 2
+        while(i <= nrow(x)) {
+            # i <- 2
+            tmp <- x
+            if(detect_overlap(tmp[i - 1, 2:3], tmp[i, 2:3]) == 1) {
+                tmp[i, ] <- NA
+                x <- tmp[complete.cases(tmp), ]
+            } else {
+                x <- tmp
+                i %+=% 1
+            }
+        }
+
+        return(x)
+    }
+)
+
+
+out
+#   seqname start end
+# 1       I     1 100
+# 2       I   101 200
+# 3       I   220 280
+# 4      II     1  50
+# 5      II   100 150
+# 6      II   300 400
+
+df
+#   seqname start end
+# 1       I     1 100
+# 2       I    20 120
+# 3       I   101 200
+# 4       I   220 280
+# 5      II     1  50
+# 6      II   100 150
+# 7      II   130 180
+# 8      II   300 400
+# 9      II   301 350