Fix Issue #216, allowing strands to be +/- 1 in plot_genes()

Author: kbroman

NEWS.md

@@ -15,12 +15,16 @@
   needed. Also, if sex is missing we assume all individuals are
   female; previously we assumed they were male. (Issue #214)
 
+- In `plot_genes()`, allow strand to be +/- 1 and not just `"+"` or
+  `"-"`. (Issue #216)
+
 ### Bug fixes
 
 - In `plot_genes()` there was a case where `stop` was used that should
   have been `end`.
 
 
+
 ## qtl2 0.30 (2022-12-02)
 
 ### Major changes

R/plot_genes.R

@@ -13,6 +13,7 @@
 #' @param start_field Character string with name of column containing the genes' start positions.
 #' @param stop_field Character string with name of column containing the genes' stop positions.
 #' @param strand_field Character string with name of column containing the genes' strands.
+#'   (The values of the corresponding field can be character strings `"+"` or `"-"`, or numeric +1 or -1.)
 #' @param name_field Character string with name of column containing the genes' names.
 #' @param ... Optional arguments passed to `plot()`.
 #'
@@ -82,6 +83,10 @@ plot_genes <-
     strand <- as.character(genes[,strand_field])
     name <- as.character(genes[,name_field])
 
+    # deal with +/- 1 for strand
+    strand[!is.na(strand) & (strand=="1" | strand=="+1")] <- "+"
+    strand[!is.na(strand) & strand=="-1"] <- "-"
+
     plot_genes_internal <-
         function(xlab=NULL, xaxs="i",
                  bgcolor="gray92", xat=NULL,