From afb196b8e758577c0b2c79a2dd17c6d9d50bc069 Mon Sep 17 00:00:00 2001
From: Nicole Kramer <nekramer@live.unc.edu>
Date: Fri, 29 Mar 2024 10:00:16 -0400
Subject: [PATCH] plotManhattan GRanges bug fix

---
 DESCRIPTION          | 4 ++--
 NEWS.md              | 5 +++++
 R/plotManhattan.R    | 5 ++---
 R/readingFunctions.R | 6 ++++++
 4 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3fe0313c..3ea39bde 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: plotgardener
 Title: Coordinate-Based Genomic Visualization Package for R
-Version: 1.8.2
-Date: 2023-12-07
+Version: 1.8.3
+Date: 2024-03-29
 Authors@R: c(person("Nicole", "Kramer", 
              email = "nekramer@live.unc.edu", 
              role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 4f86f599..6798fdf2 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# VERSION 1.8.3
+## BUG FIXES
+
+* `plotManhattan` accommodates `GRanges` data input.
+
 # VERSION 1.8.2
 ## BUG FIXES
 
diff --git a/R/plotManhattan.R b/R/plotManhattan.R
index b18a70a7..0b09a152 100644
--- a/R/plotManhattan.R
+++ b/R/plotManhattan.R
@@ -291,13 +291,12 @@ plotManhattan <- function(data, sigVal = 5e-08, chrom = NULL,
     errorcheck_plotManhattan <- function(bedfile, chrom, chromstart,
                                             chromend, object,
                                             leadSNP, fill) {
-
         ## check bedfile columns
         if (!"chrom" %in% colnames(bedfile)) {
             stop("\'chrom\' column not found in data.", call. = FALSE)
         } else {
-            if (!is(bedfile$chrom, "character")) {
-                stop("\'chrom\' column must be a character.", call. = FALSE)
+            if (!is(bedfile$chrom, "character") & !is(bedfile$chrom, "factor")) {
+                stop("\'chrom\' column must be a character or factor.", call. = FALSE)
             }
         }
         
diff --git a/R/readingFunctions.R b/R/readingFunctions.R
index 14e3d943..60622061 100644
--- a/R/readingFunctions.R
+++ b/R/readingFunctions.R
@@ -69,6 +69,12 @@ read_rangeData <- function(data, assembly, chrom = NULL,
         }
         
         
+    } else if (type == "GWAS") {
+        
+        ## Rename chrom and position columns
+        colnames(data)[seq(1, 2)] <- c("chrom", "pos")
+        ## column data types will be checked in plotManhattan errorchecks
+        
     }
     
     return(data)