Refactoring: Added helper function

R/helper.R

@@ -147,6 +147,28 @@ CheckClassTxLocConsistency <- function(obj1, obj2) {
 }
 
 
+#' Match `flank` function argument
+#' 
+#' @param flank An \code{integer} scalar or an \code{nteger} vector of length 2.
+#'
+#' @return An \code{integer} vector of length 2.
+#' 
+#' @author Maurits Evers, \email{maurits.evers@@anu.edu.au}
+MatchFlank <- function(flank) {
+
+    if (length(flank) == 1) {
+        if (flank < 0) stop("`flank` cannot be negative!")
+        return(c(-abs(flank), abs(flank)))
+    } else if (length(flank) == 2) {
+        if (any(flank < 0)) stop("`flank` cannot be negative!")
+        return(c(-abs(flank[1]), abs(flank[2])))
+    } else {
+        stop("`flank` needs to be a scalar or a vector of length 2!")
+    }
+
+}
+
+
 #' Load reference transcriptome.
 #'
 #' Load reference transcriptome. See 'Details'.

R/plot.R

@@ -965,13 +965,7 @@ PlotRelDistDistribution <- function(txLoc,
     CheckClassTxLocConsistency(txLoc, txLocRef)
 
     # Allow for variable window sizes
-    if (length(flank) == 1) {
-        flank <- c(-abs(flank), abs(flank))
-    } else if (length(flank) == 2) {
-        flank <- c(-abs(flank[1]), abs(flank[2]))
-    } else {
-        stop("`flank` needs to be a scalar or vector of length 2!")
-    }
+    flank <- MatchFlank(flank)
 
     # Get ids
     id <- GetId(txLoc)
@@ -1073,14 +1067,8 @@ PlotRelDistEnrichment <- function(txLoc1,
     CheckClassTxLocConsistency(txLoc2, txLocRef)
 
     # Allow for variable window sizes
-    if (length(flank) == 1) {
-        flank <- c(-abs(flank), abs(flank))
-    } else if (length(flank) == 2) {
-        flank <- c(-abs(flank[1]), abs(flank[2]))
-    } else {
-        stop("`flank` needs to be a scalar or vector of length 2!")
-    }
-
+    flank <- MatchFlank(flank)
+
     # Get ids
     id1 <- GetId(txLoc1)
     id2 <- GetId(txLoc2)
@@ -1277,13 +1265,7 @@ PlotRelStartStopEnrichment <- function(txLoc1,
     lstDist2 <- GetDistNearestStartStop(txLoc2)
 
     # Allow for variable window sizes
-    if (length(flank) == 1) {
-        flank <- c(-abs(flank), abs(flank))
-    } else if (length(flank) == 2) {
-        flank <- c(-abs(flank[1]), abs(flank[2]))
-    } else {
-        stop("`flank` needs to be a scalar or vector of length 2!")
-    }
+    flank <- MatchFlank(flank)
 
     # Determine figure panel layout
     par(mfrow = c(1, 2))