Merge pull request #12 from oliviaAB/main

Adding custom tracks option

NAMESPACE

@@ -1,14 +1,18 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(apply_threshold,CAN_data)
+S3method(apply_threshold,CUSTOM_data)
 S3method(apply_threshold,DE_data)
 S3method(apply_threshold,GWAS_data)
 S3method(apply_threshold,default)
 S3method(compute_chrom_length,CAN_data)
+S3method(compute_chrom_length,CUSTOM_data)
 S3method(compute_chrom_length,DE_data)
 S3method(compute_chrom_length,GWAS_data)
 export(.compute_chrom_length_genes)
+export(.compute_chrom_length_markers)
 export(CAN_data)
+export(CUSTOM_data)
 export(DE_data)
 export(GWAS_data)
 export(GWAS_data_from_gwaspoly)
@@ -17,6 +21,7 @@ export(combine_chrom_length)
 export(compute_chrom_length)
 export(create_hidecan_plot)
 export(get_example_data)
+export(hidecan_aes)
 export(hidecan_plot)
 export(hidecan_plot_from_gwaspoly)
 export(manhattan_plot)

NEWS.md

@@ -4,6 +4,15 @@
 
 * Fixed bug where specifying chromosome limits for `hidecan_plot_from_gwaspoly()` would mess up the ordering of the chromosomes in the plot.
 
+### Changes to enable custom tracks
+
+* New S3 classes to store custom genomic features: `CUSTOM_data` and `CUSTOM_data_thr`.
+
+* `create_hidecan_plot()` now accepts `CUSTOM_data_thr` objects as input, which allows users to add custom tracks to their plot. It has an additional argument `custom_aes` to handle the aesthetics for custom tracks.
+
+* Added the `hidecan_aes()` function which returns the default aesthetics for the different types of data 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/apply_threshold.R

@@ -5,16 +5,16 @@
 #' candidate genes, simply returns the list. Note that markers or genes with
 #' a missing score or log2(fold-change) will be removed from the dataset.
 #'
-#' @param x Either a `GWAS_data`, `DE_data` or `CAN_data` object.
+#' @param x Either a `GWAS_data`, `DE_data`, `CAN_data` or `CUSTOM_data` object.
 #' @param score_thr Numeric, threshold to use on markers' or genes/transcripts' score.
 #' Only markers or genes with a score equal to or higher than this threshold
 #' will be retained. Default value is 0. Ignored for `CAN_data`.
 #' @param log2fc_thr Numeric, threshold to use on the absolute value of genes/
 #' transcripts' log2(fold-change). Only genes/transcripts with an absolute
 #' log2(fold-change) equal to or higher than this threshold will be retained.
-#' Ignored for `GWAS_data` and `CAN_data`.
-#' @returns A filtered tibble (of class `GWAS_data_thr`, `DE_data_thr` or
-#' `CAN_data_thr`).
+#' Ignored for `GWAS_data`, `CAN_data` and `CUSTOM_data`.
+#' @returns A filtered tibble (of class `GWAS_data_thr`, `DE_data_thr`,
+#' `CAN_data_thr` or `CUSTOM_data_thr`).
 #' @examples
 #' x <- get_example_data()
 #'
@@ -73,6 +73,20 @@ apply_threshold.CAN_data <- function(x, score_thr = 0, log2fc_thr = 0){
   return(res)
 }
 
+#' @rdname apply_threshold
+#' @export
+apply_threshold.CUSTOM_data <- function(x, score_thr = 0, log2fc_thr = 0){
+
+  score <- NULL
+
+  res <- x |>
+    dplyr::filter(score >= score_thr)
+
+  class(res)[1] <- "CUSTOM_data_thr"
+
+  return(res)
+}
+
 #' @rdname apply_threshold
 #' @export
 apply_threshold.default <- function(x, score_thr = 0, log2fc_thr = 0){

R/compute_chromosomes_length.R

@@ -3,7 +3,7 @@
 #' Computes the length (in bp) of each chromosome as the maximum
 #' position of markers or genes on the chromosome.
 #'
-#' @param x Either a `GWAS_data`, `DE_data` or `CAN_data` object.
+#' @param x Either a `GWAS_data`, `DE_data`, `CAN_data` or `CUSTOM_data` object.
 #' @returns A tibble with two columns: `chromosome` (chromosome name) and
 #' `length` (chromosome length in base pair).
 #' @examples
@@ -20,30 +20,44 @@ compute_chrom_length <- function(x){
 #' @rdname compute_chrom_length
 #' @export
 compute_chrom_length.GWAS_data <- function(x){
-
-  chromosome <- position <- NULL
-
-  x |>
-    dplyr::group_by(chromosome) |>
-    dplyr::summarise(length = max(position),
-                     .groups = "drop")
-
+  .compute_chrom_length_markers(x)
 }
 
 #' @rdname compute_chrom_length
 #' @export
 compute_chrom_length.DE_data <- function(x){
-
   .compute_chrom_length_genes(x)
-
 }
 
 #' @rdname compute_chrom_length
 #' @export
 compute_chrom_length.CAN_data <- function(x){
-
   .compute_chrom_length_genes(x)
+}
 
+#' @rdname compute_chrom_length
+#' @export
+compute_chrom_length.CUSTOM_data <- function(x){
+  .compute_chrom_length_markers(x)
+}
+
+#' Computes chromosomes' length for a tibble of markers
+#'
+#' Computes the length (in bp) of each chromosome as the maximum
+#' position of chromosomes on the chromosome.
+#'
+#' @param x Either a `GWAS_data` or `CUSTOM_data` object.
+#' @returns A tibble with two columns: `chromosome` (chromosome name) and
+#' `length` (chromosome length in base pair).
+#' @export
+.compute_chrom_length_markers <- function(x){
+
+  chromosome <- position <- NULL
+
+  x |>
+    dplyr::group_by(chromosome) |>
+    dplyr::summarise(length = max(position),
+                     .groups = "drop")
 }
 
 #' Computes chromosomes' length for a tibble of genes
@@ -73,7 +87,7 @@ compute_chrom_length.CAN_data <- function(x){
 #' Computes the length (in bp) of each chromosome from a list of GWAS and
 #' DE results as well as candidate gene lists.
 #'
-#' @param x A list of `GWAS_data`, `DE_data` or `CAN_data` objects.
+#' @param x A list of `GWAS_data`, `DE_data`, `CAN_data` or `CUSTOM_data` objects.
 #' @returns A tibble with two columns: `chromosome` (chromosome name) and
 #' `length` (chromosome length in base pair).
 #' @examples