From 97c881008b736e7513cf3f30b8fb8f65f9a64f06 Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Wed, 10 Jan 2024 14:36:16 +0100
Subject: [PATCH] fix: as.matrix returns sparse by default, use as(x,
 'dgTMatrix') for sparse

---
 R/coerce.R                                  | 10 +++++++++-
 man/as.Rd                                   |  2 +-
 tests/testthat/test-HiCExperiment-methods.R | 16 +++++++++++++---
 vignettes/HiCExperiment.Rmd                 |  3 ++-
 4 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/R/coerce.R b/R/coerce.R
index 6ee69ff..827c96f 100644
--- a/R/coerce.R
+++ b/R/coerce.R
@@ -90,6 +90,14 @@ setAs("HiCExperiment", "ContactMatrix", function(from) {
 #' @name as
 
 setAs("HiCExperiment", "matrix", function(from) {
+    as(from, "ContactMatrix") |> cm2matrix(sparse = FALSE)
+})
+
+
+#' @export
+#' @name as
+
+setAs("HiCExperiment", "dgTMatrix", function(from) {
     as(from, "ContactMatrix") |> cm2matrix(sparse = TRUE)
 })
 
@@ -109,7 +117,7 @@ setAs("HiCExperiment", "data.frame", function(from) {
 #' @export
 #' @name as
 
-setMethod("as.matrix", "HiCExperiment", function(x, use.scores = "balanced", sparse = TRUE) {
+setMethod("as.matrix", "HiCExperiment", function(x, use.scores = "balanced", sparse = FALSE) {
     interactions(x) |> gi2cm(use.scores = use.scores) |> cm2matrix(sparse = sparse)
 })
 
diff --git a/man/as.Rd b/man/as.Rd
index 8ab49e8..30057d5 100644
--- a/man/as.Rd
+++ b/man/as.Rd
@@ -14,7 +14,7 @@
 \alias{df2gi}
 \title{Coercing functions}
 \usage{
-\S4method{as.matrix}{HiCExperiment}(x, use.scores = "balanced", sparse = TRUE)
+\S4method{as.matrix}{HiCExperiment}(x, use.scores = "balanced", sparse = FALSE)
 
 \S4method{as.data.frame}{HiCExperiment}(x)
 
diff --git a/tests/testthat/test-HiCExperiment-methods.R b/tests/testthat/test-HiCExperiment-methods.R
index 8bac85a..28b0c33 100644
--- a/tests/testthat/test-HiCExperiment-methods.R
+++ b/tests/testthat/test-HiCExperiment-methods.R
@@ -95,13 +95,23 @@ test_that("coerce works", {
     expect_s4_class({
         as(contacts_yeast, 'ContactMatrix')
     }, 'ContactMatrix')
-    expect_true(is.matrix(base::as.matrix(as.matrix(contacts_yeast))))
+    expect_true({
+        is.matrix(as(contacts_yeast, 'matrix'))
+    })
+    expect_false({
+        is.matrix(as(contacts_yeast, 'dgTMatrix'))
+    })
     expect_s4_class({
-        as(contacts_yeast, 'matrix')
+        as(contacts_yeast, 'dgTMatrix')
     }, 'dgTMatrix')
     expect_s4_class({
-        as.matrix(contacts_yeast)
+        as.matrix(contacts_yeast, sparse = TRUE)
     }, 'dgTMatrix')
+    expect_true({
+        is.matrix(
+            as.matrix(contacts_yeast, sparse = FALSE)
+        )
+    })
     expect_s3_class({
         df <- as(contacts_yeast, 'data.frame')
     }, 'data.frame')
diff --git a/vignettes/HiCExperiment.Rmd b/vignettes/HiCExperiment.Rmd
index 898e92a..520654b 100644
--- a/vignettes/HiCExperiment.Rmd
+++ b/vignettes/HiCExperiment.Rmd
@@ -116,8 +116,9 @@ The implemented `import()` methods allow one to import Hi-C matrix files in R as
 `HiCExperiment` objects. 
 
 ```{r import, eval = FALSE}
+## Change <path/to/contact_matrix>.cool accordingly
 hic <- import(
-    "path/to/contact_matrix.cool", 
+    "<path/to/contact_matrix>.cool", 
     focus = "chr:start-end", 
     resolution = ...
 )