pre-commit run --all-files

R/hictkR-exports.R

@@ -30,7 +30,6 @@ loadModule(module = "hictkR", TRUE)
 #' File("interactions.mcool", 100000)
 #' File("interactions.hic", 100000)
 #' }
-
 File <-
   function(path,
            resolution = NULL,
@@ -50,7 +49,6 @@ File <-
 #' \dontrun{
 #' MultiResFile("interactions.mcool")
 #' }
-
 MultiResFile <- function(path) {
   return(new(RcppMultiResFile, path))
 }
@@ -63,7 +61,6 @@ MultiResFile <- function(path) {
 #' \dontrun{
 #' SingleCellFile("interactions.scool")
 #' }
-
 SingleCellFile <- function(path) {
   return(new(RcppSingleCellFile, path))
 }
@@ -92,21 +89,25 @@ SingleCellFile <- function(path) {
 #' @returns a DataFrame or Matrix object with the interactions for the given query.
 #' @examples
 #' \dontrun{
-#' f <- File("interactions.hic",
-#'           1000000)
-#' fetch(f)                             # Fetch genome-wide interactions
-#' fetch(f, "chr2L")                    # Fetch interactions overlapping a symmetric query
+#' f <- File(
+#'   "interactions.hic",
+#'   1000000
+#' )
+#' fetch(f) # Fetch genome-wide interactions
+#' fetch(f, "chr2L") # Fetch interactions overlapping a symmetric query
+#' fetch(
+#'   f,
+#'   "chr2L:0-10,000,000",
+#'   "chr3L:10,000,000-20,000,000"
+#' ) # Fetch interactions overlapping an asymmetric query
+#' fetch(f, normalization = "ICE") # Fetch ICE-normalized interactions
+#' fetch(f, join = TRUE) # Fetch interactions together with their genomic coordinates
 #' fetch(f,
-#'       "chr2L:0-10,000,000",
-#'       "chr3L:10,000,000-20,000,000") # Fetch interactions overlapping an asymmetric query
-#' fetch(f, normalization="ICE")        # Fetch ICE-normalized interactions
-#' fetch(f, join=TRUE)                  # Fetch interactions together with their genomic coordinates
-#' fetch(f,
-#'       "chr1\t0\t10000000",
-#'       query_type="BED")              # Fetch interactions given a query in BED format
-#' fetch(f, type="dense")               # Fetch interactions in dense format (i.e. as a Matrix)
+#'   "chr1\t0\t10000000",
+#'   query_type = "BED"
+#' ) # Fetch interactions given a query in BED format
+#' fetch(f, type = "dense") # Fetch interactions in dense format (i.e. as a Matrix)
 #' }
-
 fetch <-
   function(file,
            range1 = "",
@@ -138,11 +139,10 @@ fetch <-
 #' hictkR_open("interactions.cool")
 #' hictkR_open("interactions.mcool")
 #' hictkR_open("interactions.scool")
-#' hictkR_open("interactions.mcool", resolution=10000)
-#' hictkR_open("interactions.hic", resolution=10000)
-#' hictkR_open("interactions.scool", cell="id_0001")
+#' hictkR_open("interactions.mcool", resolution = 10000)
+#' hictkR_open("interactions.hic", resolution = 10000)
+#' hictkR_open("interactions.scool", cell = "id_0001")
 #' }
-
 hictkR_open <- function(path,
                         resolution = NULL,
                         cell = NULL) {

tests/testthat/test-fetch-dense.R

@@ -2,15 +2,17 @@
 #
 # SPDX-License-Identifier: MIT
 
-test_files <- c(test_path("..", "data", "hic_test_file.hic"),
-                test_path("..", "data", "cooler_test_file.mcool"))
+test_files <- c(
+  test_path("..", "data", "hic_test_file.hic"),
+  test_path("..", "data", "cooler_test_file.mcool")
+)
 
 
 for (path in test_files) {
   test_that("HiCFile: fetch (dense) genome-wide", {
     f <- File(path, 100000)
 
-    m <- fetch(f, type="dense")
+    m <- fetch(f, type = "dense")
 
     shape <- dim(m)
     sum_ <- sum(m)
@@ -22,7 +24,7 @@ for (path in test_files) {
   test_that("HiCFile: fetch (dense) symmetric cis", {
     f <- File(path, 100000)
 
-    m <- fetch(f, "chr2R:10,000,000-15,000,000", type="dense")
+    m <- fetch(f, "chr2R:10,000,000-15,000,000", type = "dense")
 
     shape <- dim(m)
     sum_ <- sum(m)
@@ -34,7 +36,7 @@ for (path in test_files) {
   test_that("HiCFile: fetch (dense) asymmetric cis", {
     f <- File(path, 100000)
 
-    m <- fetch(f, "chr2L:0-10,000,000", "chr2L:5,000,000-20,000,000", type="dense")
+    m <- fetch(f, "chr2L:0-10,000,000", "chr2L:5,000,000-20,000,000", type = "dense")
 
     shape <- dim(m)
     sum_ <- sum(m)
@@ -43,15 +45,15 @@ for (path in test_files) {
     expect_equal(sum_, 6287451)
 
 
-    m <- fetch(f, "chr2L:0-10,000,000", "chr2L:10,000,000-20,000,000", type="dense")
+    m <- fetch(f, "chr2L:0-10,000,000", "chr2L:10,000,000-20,000,000", type = "dense")
 
     shape <- dim(m)
     sum_ <- sum(m)
 
     expect_equal(shape, c(100, 100))
     expect_equal(sum_, 761223)
 
-    m <- fetch(f, "chr2L:0-10,000,000", "chr2L:0-15,000,000", type="dense")
+    m <- fetch(f, "chr2L:0-10,000,000", "chr2L:0-15,000,000", type = "dense")
 
     shape <- dim(m)
     sum_ <- sum(m)
@@ -63,7 +65,7 @@ for (path in test_files) {
   test_that("HiCFile: fetch (dense) cis BED queries", {
     f <- File(path, 100000)
 
-    m <- fetch(f, "chr2R\t10000000\t15000000", type="dense", query_type="BED")
+    m <- fetch(f, "chr2R\t10000000\t15000000", type = "dense", query_type = "BED")
 
     shape <- dim(m)
     sum_ <- sum(m)
@@ -75,7 +77,7 @@ for (path in test_files) {
   test_that("HiCFile: fetch (dense) trans", {
     f <- File(path, 100000)
 
-    m <- fetch(f, "chr2R:10,000,000-15,000,000", "chrX:0-10,000,000", type="dense")
+    m <- fetch(f, "chr2R:10,000,000-15,000,000", "chrX:0-10,000,000", type = "dense")
 
     shape <- dim(m)
     sum_ <- sum(m)
@@ -87,7 +89,7 @@ for (path in test_files) {
   test_that("HiCFile: fetch (dense) trans BED queries", {
     f <- File(path, 100000)
 
-    m <- fetch(f, "chr2R\t10000000\t15000000", "chrX\t0\t10000000", type="dense", query_type="BED")
+    m <- fetch(f, "chr2R\t10000000\t15000000", "chrX\t0\t10000000", type = "dense", query_type = "BED")
 
     shape <- dim(m)
     sum_ <- sum(m)

tests/testthat/test-fetch-df.R

@@ -2,8 +2,10 @@
 #
 # SPDX-License-Identifier: MIT
 
-test_files <- c(test_path("..", "data", "hic_test_file.hic"),
-                test_path("..", "data", "cooler_test_file.mcool"))
+test_files <- c(
+  test_path("..", "data", "hic_test_file.hic"),
+  test_path("..", "data", "cooler_test_file.mcool")
+)
 
 for (path in test_files) {
   test_that("HiCFile: fetch (DF) genome-wide", {
@@ -31,7 +33,7 @@ for (path in test_files) {
   test_that("HiCFile: fetch (DF) cis bg2", {
     f <- File(path, 100000)
 
-    df <- fetch(f, "chr2R:10,000,000-15,000,000", join=TRUE)
+    df <- fetch(f, "chr2R:10,000,000-15,000,000", join = TRUE)
     sum_ <- sum(df$count)
     num_columns <- length(df)
 
@@ -42,7 +44,7 @@ for (path in test_files) {
   test_that("HiCFile: fetch (DF) cis BED queries", {
     f <- File(path, 100000)
 
-    df <- fetch(f, "chr2R\t10000000\t15000000", query_type="BED")
+    df <- fetch(f, "chr2R\t10000000\t15000000", query_type = "BED")
     nnz <- length(df$count)
 
     expect_equal(nnz, 1275)
@@ -62,7 +64,7 @@ for (path in test_files) {
   test_that("HiCFile: fetch (DF) trans bg2", {
     f <- File(path, 100000)
 
-    df <- fetch(f, "chr2R:10,000,000-15,000,000", "chrX:0-10,000,000", join=TRUE)
+    df <- fetch(f, "chr2R:10,000,000-15,000,000", "chrX:0-10,000,000", join = TRUE)
     sum_ <- sum(df$count)
     num_columns <- length(df)
 
@@ -73,7 +75,7 @@ for (path in test_files) {
   test_that("HiCFile: fetch (DF) cis: BED queries", {
     f <- File(path, 100000)
 
-    df <- fetch(f, "chr2R\t10000000\t15000000", "chrX\t0\t10000000", query_type="BED")
+    df <- fetch(f, "chr2R\t10000000\t15000000", "chrX\t0\t10000000", query_type = "BED")
     nnz <- length(df$count)
 
     expect_equal(nnz, 4995)
@@ -83,14 +85,13 @@ for (path in test_files) {
     f <- File(path, 100000)
 
     if (f$is_cooler) {
-      df <- fetch(f, "chr2R:10,000,000-15,000,000", normalization="weight")
+      df <- fetch(f, "chr2R:10,000,000-15,000,000", normalization = "weight")
     } else {
-      df <- fetch(f, "chr2R:10,000,000-15,000,000", normalization="ICE")
+      df <- fetch(f, "chr2R:10,000,000-15,000,000", normalization = "ICE")
     }
 
     sum_ <- sum(df$count)
 
     expect_equal(sum_, 59.349524704033215)
   })
-
 }

tests/testthat/test-file-accessors.R

@@ -37,7 +37,7 @@ test_that("File: chromosomes accessor", {
   path2 <- test_path("..", "data", "chromosomes.tsv.gz")
 
   chroms <- File(path1, 100000)$chromosomes
-  expected_chroms <- read.csv(path2, sep="\t")
+  expected_chroms <- read.csv(path2, sep = "\t")
   expect_equal(chroms, expected_chroms)
 })
 
@@ -48,7 +48,7 @@ test_that("File: bins accessor", {
 
   bins1 <- File(path1, 100000)$bins
   bins2 <- File(path2, 100000)$bins
-  expected_bins <- read.csv(path3, sep="\t", stringsAsFactors=FALSE)
+  expected_bins <- read.csv(path3, sep = "\t", stringsAsFactors = FALSE)
 
   bins1$chrom <- as.character(bins1$chrom)
   bins2$chrom <- as.character(bins2$chrom)

tests/testthat/test-hictkR-open.R

@@ -5,7 +5,7 @@
 hic_file <- test_path("..", "data", "hic_test_file.hic")
 mcool_file <- test_path("..", "data", "cooler_test_file.mcool")
 scool_file <- test_path("..", "data", "cooler_test_file.scool")
-cool_file <- paste(test_path("..", "data", "cooler_test_file.mcool"), "::/resolutions/100000", sep="")
+cool_file <- paste(test_path("..", "data", "cooler_test_file.mcool"), "::/resolutions/100000", sep = "")
 
 test_that("hicrkR_open: .hic", {
   expected <- class(File(hic_file, 100000))
@@ -20,19 +20,19 @@ test_that("hicrkR_open: .cool", {
   f <- hictkR_open(cool_file)
   expect_equal(expected, class(f))
 
-  f <- hictkR_open(mcool_file, resolution=100000)
+  f <- hictkR_open(mcool_file, resolution = 100000)
   expect_equal(expected, class(f))
 
-  f <- hictkR_open(scool_file, cell="GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool")
+  f <- hictkR_open(scool_file, cell = "GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool")
   expect_equal(expected, class(f))
 
   mclr <- MultiResFile(mcool_file)
   sclr <- SingleCellFile(scool_file)
 
-  f <- hictkR_open(mclr, resolution=100000)
+  f <- hictkR_open(mclr, resolution = 100000)
   expect_equal(expected, class(f))
 
-  f <- hictkR_open(sclr, cell="GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool")
+  f <- hictkR_open(sclr, cell = "GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool")
   expect_equal(expected, class(f))
 })
 

tests/testthat/test-multiresolution-file-accessors.R

@@ -15,7 +15,7 @@ test_that("MultiResFile: chromosomes accessor", {
   path2 <- test_path("..", "data", "chromosomes.tsv.gz")
 
   chroms <- MultiResFile(path1)$chromosomes
-  expected_chroms <- read.csv(path2, sep="\t")
+  expected_chroms <- read.csv(path2, sep = "\t")
   expect_equal(chroms, expected_chroms)
 })
 

tests/testthat/test-singlecell-file-accessors.R

@@ -33,10 +33,14 @@ test_that("SingleCellFile: chromosomes accessor", {
 
 test_that("SingleCellFile: file cells accessor", {
   f <- SingleCellFile(scool_file)
-  expect_equal(f$cells,
-               c("GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool",
-                 "GSM2687249_41670_GGCTAC-R1-DpnII.100000.cool",
-                 "GSM2687250_41671_TTAGGC-R1-DpnII.100000.cool",
-                 "GSM2687251_41672_AGTTCC-R1-DpnII.100000.cool",
-                 "GSM2687252_41673_CCGTCC-R1-DpnII.100000.cool"))
+  expect_equal(
+    f$cells,
+    c(
+      "GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool",
+      "GSM2687249_41670_GGCTAC-R1-DpnII.100000.cool",
+      "GSM2687250_41671_TTAGGC-R1-DpnII.100000.cool",
+      "GSM2687251_41672_AGTTCC-R1-DpnII.100000.cool",
+      "GSM2687252_41673_CCGTCC-R1-DpnII.100000.cool"
+    )
+  )
 })