From 56e13df87a9257f13f48abbb329bf975c4892df0 Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Tue, 12 Dec 2023 21:24:53 +0100
Subject: [PATCH] fix: add an expand method from tidyr generic rather than
 S4Vectors

---
 R/expand.R                                     | 18 +++++++++---------
 man/expand.Rd                                  |  4 ++--
 .../testthat/test-compute-filter-import-plot.R |  2 +-
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/expand.R b/R/expand.R
index f2c2c14..8872ab1 100644
--- a/R/expand.R
+++ b/R/expand.R
@@ -12,7 +12,7 @@
 #' @aliases expand,CoverageExperiment-method
 #' @rdname expand
 #' 
-#' @param x a `CoverageExperiment` object
+#' @param data a `CoverageExperiment` object
 #' @param ...,.name_repair ignored
 #' @return a `tibble` object
 #' 
@@ -24,18 +24,18 @@
 #' 
 #' expand(ce)
 
-expand.CoverageExperiment <- function(x, ..., .name_repair = NULL) {
-    tracks <- colData(x)$track
-    features <- rowData(x)$features
-    w <- width(rowRanges(x)[[1]])[[1]]
-    bin <- w / ncol(assay(x, "coverage")[1, 1][[1]])
+expand.CoverageExperiment <- function(data, ..., .name_repair = NULL) {
+    tracks <- colData(data)$track
+    features <- rowData(data)$features
+    w <- width(rowRanges(data)[[1]])[[1]]
+    bin <- w / ncol(assay(data, "coverage")[1, 1][[1]])
     df <- lapply(features, function(f) {
-        rr <- rowRanges(x)[[f]]
+        rr <- rowRanges(data)[[f]]
         rrdf <- as.data.frame(rr)
         coord <- lapply(seq_len(nrow(rrdf)), function(K) seq(rrdf[K, 'start'], rrdf[K, 'end'], by = bin)) |> unlist()
         coord.scaled <- lapply(seq_len(nrow(rrdf)), function(K) seq(-w/2, w/2-1, by = bin)) |> unlist()
         lapply(tracks, function(t) {
-            m <- assay(x, "coverage")[f, t][[1]] |> 
+            m <- assay(data, "coverage")[f, t][[1]] |> 
                 as.data.frame() |>
                 dplyr::mutate(
                     track = t, features = f, 
@@ -55,7 +55,7 @@ expand.CoverageExperiment <- function(x, ..., .name_repair = NULL) {
         }) |> dplyr::bind_rows()
     }) |> 
         dplyr::bind_rows() |> 
-        dplyr::left_join(colData(x) |> as.data.frame(), by = 'track') |> 
+        dplyr::left_join(colData(data) |> as.data.frame(), by = 'track') |> 
         dplyr::group_by(track, features, ranges)
     return(df)
 }
diff --git a/man/expand.Rd b/man/expand.Rd
index abb9022..f74eaf0 100644
--- a/man/expand.Rd
+++ b/man/expand.Rd
@@ -6,10 +6,10 @@
 \alias{expand,CoverageExperiment-method}
 \title{Expand a CoverageExperiment object}
 \usage{
-\method{expand}{CoverageExperiment}(x, ..., .name_repair = NULL)
+\method{expand}{CoverageExperiment}(data, ..., .name_repair = NULL)
 }
 \arguments{
-\item{x}{a \code{CoverageExperiment} object}
+\item{data}{a \code{CoverageExperiment} object}
 
 \item{..., .name_repair}{ignored}
 }
diff --git a/tests/testthat/test-compute-filter-import-plot.R b/tests/testthat/test-compute-filter-import-plot.R
index 02d7a9a..e0f1457 100644
--- a/tests/testthat/test-compute-filter-import-plot.R
+++ b/tests/testthat/test-compute-filter-import-plot.R
@@ -187,7 +187,7 @@ test_that("expand method works", {
     CE <- CoverageExperiment(
         tracks, features, width = 100, scale = TRUE, center = TRUE
     )
-    expect_true(all(dim(expand(CE)) == c(402600, 7)))
+    expect_true(all(dim(expand(CE)) == c(402600, 8)))
     expect_true(all(colnames(expand(CE)) == c("track", "features", "chr", "ranges", "strand", "coord", "coverage", "coord.scaled")))
 })