Merge pull request #110 from PhanstielLab/RELEASE_3_18_patch3

plotManhattan GRanges bug fix

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 = "[email protected]", 
              role = c("aut", "cre"),

NEWS.md

@@ -1,3 +1,8 @@
+# VERSION 1.8.3
+## BUG FIXES
+
+* `plotManhattan` accommodates `GRanges` data input.
+
 # VERSION 1.8.2
 ## BUG FIXES
 

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)
             }
         }
 

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)