Merge pull request #11 from oliviaAB/main

Fixed bug GWASpoly chromosome ordering with limits

DESCRIPTION

@@ -14,7 +14,7 @@ URL: https://plantandfoodresearch.github.io/hidecan/, https://github.com/Plantan
 BugReports: https://github.com/PlantandFoodResearch/hidecan/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 2.10)
 Imports: 

NEWS.md

@@ -2,6 +2,8 @@
 
 * Added the `manhattan_plot()` function to generate Manhattan plots from a table of GWAS results.
 
+* Fixed bug where specifying chromosome limits for `hidecan_plot_from_gwaspoly()` would mess up the ordering of the chromosomes in the plot.
+
 # hidecan 1.1.0
 
 * Removed `get_gwaspoly_example_data()` function so that the package doesn't depend on GWASpoly (for CRAN submission)

R/create_hidecan_plot.R

@@ -187,11 +187,11 @@ create_hidecan_plot <- function(x,
   ## Now filter both toplot and chrom_lenght to only the desired chromosomes
   toplot <- toplot |>
     dplyr::filter(chromosome %in% chroms) |>
-    dplyr::mutate(chromosome = factor(chromosome, levels = chroms))
+    dplyr::mutate(chromosome = factor(chromosome, levels = chroms, ordered = FALSE))
 
   chrom_length <- chrom_length |>
     dplyr::filter(chromosome %in% chroms) |>
-    dplyr::mutate(chromosome = factor(chromosome, levels = chroms))
+    dplyr::mutate(chromosome = factor(chromosome, levels = chroms, ordered = FALSE))
 
   toplot_chroms <- chrom_length |>
     dplyr::mutate(position_mb = length / 1e6) |>
@@ -231,7 +231,8 @@ create_hidecan_plot <- function(x,
           ~ tibble::tibble(lower_limit_mb = .x[[1]],
                            upper_limit_mb = .x[[2]]),
           .id = "chromosome"
-        ),
+        ) |>
+          dplyr::mutate(chromosome = factor(chromosome, levels = chroms)),
         by = "chromosome"
       ) |>
       tidyr::replace_na(list(lower_limit_mb = 0)) |>