solve styling issues and rebuild docs

dynverse · Sep 5, 2024 · f7ff341 · f7ff341
1 parent cf5e52b
commit f7ff341
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Showing 21 changed files with 119 additions and 116 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -47,7 +47,7 @@ Suggests:
     rmarkdown
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Config/reticulate:
   list(
     packages = list(

diff --git a/R/class_anndata.R b/R/class_anndata.R
@@ -106,7 +106,7 @@
 #'   uns = list(a = 1, b = 2, c = list(c.a = 3, c.b = 4))
 #' )
 #'
-#' value <- matrix(c(1,2,3,4), nrow = 2)
+#' value <- matrix(c(1, 2, 3, 4), nrow = 2)
 #' ad$X <- value
 #' ad$X
 #'
@@ -125,21 +125,20 @@
 #' colnames(ad)
 #' }
 AnnData <- function(
-  X = NULL,
-  obs = NULL,
-  var = NULL,
-  uns = NULL,
-  obsm = NULL,
-  varm = NULL,
-  layers = NULL,
-  raw = NULL,
-  dtype = "float32",
-  shape = NULL,
-  filename = NULL,
-  filemode = NULL,
-  obsp = NULL,
-  varp = NULL
-) {
+    X = NULL,
+    obs = NULL,
+    var = NULL,
+    uns = NULL,
+    obsm = NULL,
+    varm = NULL,
+    layers = NULL,
+    raw = NULL,
+    dtype = "float32",
+    shape = NULL,
+    filename = NULL,
+    filemode = NULL,
+    obsp = NULL,
+    varp = NULL) {
   # check nrow size
   nrow <- nrow(X)
   if (is.null(nrow)) nrow <- nrow(obs)
@@ -980,9 +979,9 @@ AnnDataR6 <- R6::R6Class(
 #' as.data.frame(ad, layer = "unspliced")
 #' as.matrix(ad)
 #' as.matrix(ad, layer = "unspliced")
-#' ad[2,,drop=FALSE]
-#' ad[,-1]
-#' ad[,c("var1", "var2")]
+#' ad[2, , drop = FALSE]
+#' ad[, -1]
+#' ad[, c("var1", "var2")]
 #' }
 dimnames.AnnDataR6 <- function(x) {
   list(
@@ -995,12 +994,14 @@ dimnames.AnnDataR6 <- function(x) {
 #' @export
 `dimnames<-.AnnDataR6` <- function(x, value) {
   d <- dim(x)
-  if (!is.list(value) || length(value) != 2L)
+  if (!is.list(value) || length(value) != 2L) {
     stop("invalid 'dimnames' given for AnnData")
+  }
   # value[[1L]] <- as.character(value[[1L]])
   # value[[2L]] <- as.character(value[[2L]])
-  if (d[[1L]] != length(value[[1L]]) || d[[2L]] != length(value[[2L]]))
+  if (d[[1L]] != length(value[[1L]]) || d[[2L]] != length(value[[2L]])) {
     stop("invalid 'dimnames' given for AnnData")
+  }
   x$obs_names <- value[[1L]]
   x$var_names <- value[[2L]]
   x

diff --git a/R/class_layers.R b/R/class_layers.R
@@ -25,9 +25,8 @@
 #' names(ad$layers)
 #' }
 Layers <- function(
-  parent,
-  vals = NULL
-) {
+    parent,
+    vals = NULL) {
   python_anndata <- reticulate::import("anndata", convert = FALSE)
 
   obj <- python_anndata$Layers(
@@ -124,7 +123,6 @@ LayersR6 <- R6::R6Class(
     .get_py_object = function() {
       private$.layers
     }
-
   ),
   active = list(
     #' @field parent Reference to parent AnnData view

diff --git a/R/class_raw.R b/R/class_raw.R
@@ -41,11 +41,10 @@
 #' ad$raw[]
 #' }
 Raw <- function(
-  adata,
-  X = NULL,
-  var = NULL,
-  varm = NULL
-) {
+    adata,
+    X = NULL,
+    var = NULL,
+    varm = NULL) {
   python_anndata <- reticulate::import("anndata", convert = FALSE)
 
   raw <- python_anndata$Raw(
@@ -167,7 +166,7 @@ RawR6 <- R6::R6Class(
   active = list(
     #' @field X Data matrix of shape `n_obs` × `n_vars`.
     X = function() {
-        py_to_r_ifneedbe(private$.raw$X)
+      py_to_r_ifneedbe(private$.raw$X)
     },
     #' @field n_obs Number of observations.
     n_obs = function() {
@@ -238,9 +237,9 @@ RawR6 <- R6::R6Class(
 #' dimnames(ad$raw)
 #' dim(ad$raw)
 #' as.matrix(ad$raw)
-#' ad$raw[2,,drop=FALSE]
-#' ad$raw[,-1]
-#' ad$raw[,c("var1", "var2")]
+#' ad$raw[2, , drop = FALSE]
+#' ad$raw[, -1]
+#' ad$raw[, c("var1", "var2")]
 #' }
 dimnames.RawR6 <- function(x) {
   list(

diff --git a/R/concat.R b/R/concat.R
@@ -108,17 +108,16 @@
 #' concat(list(a, b, c), uns_merge = "only")$uns
 #' }
 concat <- function(
-  adatas,
-  axis = 0L,
-  join = "inner",
-  merge = NULL,
-  uns_merge = NULL,
-  label = NULL,
-  keys = NULL,
-  index_unique = NULL,
-  fill_value = NULL,
-  pairwise = FALSE
-) {
+    adatas,
+    axis = 0L,
+    join = "inner",
+    merge = NULL,
+    uns_merge = NULL,
+    label = NULL,
+    keys = NULL,
+    index_unique = NULL,
+    fill_value = NULL,
+    pairwise = FALSE) {
   assert_that(
     is.list(adatas),
     all(sapply(adatas, inherits, "AnnDataR6"))

diff --git a/R/package.R b/R/package.R
@@ -90,7 +90,7 @@
 #'
 #' ad$uns["b"]
 #'
-#' ad[,c("var1", "var2")]
+#' ad[, c("var1", "var2")]
 #' ad[-1, , drop = FALSE]
 #' ad[, 2] <- 10
 #' }

diff --git a/R/read_h5ad.R b/R/read_h5ad.R
@@ -12,9 +12,8 @@
 #' ad <- read_h5ad("example_formats/pbmc_1k_protein_v3_processed.h5ad")
 #' }
 read_h5ad <- function(
-  filename,
-  backed = NULL
-) {
+    filename,
+    backed = NULL) {
   python_anndata <- reticulate::import("anndata", convert = FALSE)
   filename <- normalizePath(filename, mustWork = FALSE)
   py_to_r_ifneedbe(python_anndata$read_h5ad(

diff --git a/R/read_loom.R b/R/read_loom.R
@@ -23,17 +23,16 @@
 #' ad <- read_loom("dataset.loom")
 #' }
 read_loom <- function(
-  filename,
-  sparse = TRUE,
-  cleanup = FALSE,
-  X_name = "spliced",
-  obs_names = "CellID",
-  obsm_names = NULL,
-  var_names = "Gene",
-  varm_names = NULL,
-  dtype = "float32",
-  ...
-) {
+    filename,
+    sparse = TRUE,
+    cleanup = FALSE,
+    X_name = "spliced",
+    obs_names = "CellID",
+    obsm_names = NULL,
+    var_names = "Gene",
+    varm_names = NULL,
+    dtype = "float32",
+    ...) {
   python_anndata <- reticulate::import("anndata", convert = FALSE)
   filename <- normalizePath(filename, mustWork = FALSE)
   py_to_r_ifneedbe(python_anndata$read_loom(

diff --git a/R/reticulate_conversions.R b/R/reticulate_conversions.R
@@ -93,7 +93,7 @@ py_to_r.collections.abc.KeysView <- function(x) {
 #' @importFrom Matrix sparseMatrix
 py_to_r.scipy.sparse.csc.csc_matrix <- function(x) {
   Matrix::sparseMatrix(
-    i = as.integer(py_to_r_ifneedbe(x$indices))+1,
+    i = as.integer(py_to_r_ifneedbe(x$indices)) + 1,
     p = as.integer(py_to_r_ifneedbe(x$indptr)),
     x = as.vector(py_to_r_ifneedbe(x$data)),
     dims = as.integer(dim(x))

diff --git a/R/write_csvs.R b/R/write_csvs.R
@@ -34,4 +34,3 @@ write_csvs <- function(anndata, dirname, skip_data = TRUE, sep = ",") {
     sep = sep
   )))
 }
-
diff --git a/R/write_h5ad.R b/R/write_h5ad.R
@@ -38,4 +38,3 @@ write_h5ad <- function(anndata, filename, compression = NULL, compression_opts =
     as_dense = as_dense
   )))
 }
-
diff --git a/README.Rmd b/README.Rmd
@@ -67,7 +67,7 @@ ad <- read_h5ad("example_formats/pbmc_1k_protein_v3_processed.h5ad")
 
 ad
 
-Matrix::rowMeans(ad$X[1:10,])
+Matrix::rowMeans(ad$X[1:10, ])
 ```
 
 
@@ -78,13 +78,13 @@ Check out any of the other vignettes by clicking any of the links below:
 walk(
   list.files("vignettes", pattern = "*.Rmd", recursive = TRUE),
   function(file) {
-    title <- 
-      read_lines(paste0("vignettes/", file)) %>% 
-      keep(~grepl("^title: ", .)) %>% 
+    title <-
+      read_lines(paste0("vignettes/", file)) %>%
+      keep(~ grepl("^title: ", .)) %>%
       gsub("title: \"(.*)\"", "\\1", .)
     vignette_name <- gsub("\\.Rmd", "", file)
     html_name <- gsub("\\.Rmd", ".html", file)
-    
+
     cat("* [", title, "](https://anndata.dynverse.org/articles/", html_name, ")\n", sep = "")
   }
 )

diff --git a/man/AnnData.Rd b/man/AnnData.Rd
diff --git a/man/AnnDataHelpers.Rd b/man/AnnDataHelpers.Rd
diff --git a/man/RawHelpers.Rd b/man/RawHelpers.Rd
diff --git a/man/anndata-package.Rd b/man/anndata-package.Rd
diff --git a/tests/testthat/helper-gen_adata.R b/tests/testthat/helper-gen_adata.R
@@ -32,11 +32,10 @@ gen_typed_df <- function(n, index = NULL) {
 }
 
 gen_adata <- function(
-  shape,
-  obsm_types = c("matrix", "sparseMatrix", "data.frame"),
-  varm_types = c("matrix", "sparseMatrix", "data.frame"),
-  layer_types = c("matrix", "sparseMatrix")
-) {
+    shape,
+    obsm_types = c("matrix", "sparseMatrix", "data.frame"),
+    varm_types = c("matrix", "sparseMatrix", "data.frame"),
+    layer_types = c("matrix", "sparseMatrix")) {
   M <- shape[[1]]
   N <- shape[[2]]
 
@@ -45,8 +44,10 @@ gen_adata <- function(
   obs <- gen_typed_df(M, obs_names)
   var <- gen_typed_df(N, var_names)
   # for #147
-  obs$obs_cat <- obs$cat; obs$cat <- NULL
-  var$var_cat <- var$cat; var$cat <- NULL
+  obs$obs_cat <- obs$cat
+  obs$cat <- NULL
+  var$var_cat <- var$cat
+  var$cat <- NULL
 
   obsm <- list(
     array = matrix(runif(M * 50), nrow = M),
@@ -83,7 +84,7 @@ gen_adata <- function(
     sparse = Matrix::rsparsematrix(N, N, density = 0.1)
   )
   uns <- list(
-    O_recarray = gen_vstr_recarray(N, 5)#,
+    O_recarray = gen_vstr_recarray(N, 5) # ,
     # U_recarray=gen_vstr_recarray(N, 5, "U4")
   )
 

diff --git a/tests/testthat/test-anndata.R b/tests/testthat/test-anndata.R
@@ -65,8 +65,8 @@ test_that("test common R functions", {
 
   expect_true(all(as.data.frame(ad, layer = "unspliced") == list(var1 = 8:9, var2 = 10:11, var3 = 12:13)))
 
-  expect_equal(ad$X[,1], c(s1 = 1, s2 = 2))
-  expect_equal(ad$X[1,], c(var1 = 1, var2 = 3, var3 = 5))
+  expect_equal(ad$X[, 1], c(s1 = 1, s2 = 2))
+  expect_equal(ad$X[1, ], c(var1 = 1, var2 = 3, var3 = 5))
 })
 
 test_that("anndata works with sparse data", {
Original file line number	Diff line number	Diff line change
Expand Up		@@ -34,4 +34,3 @@ write_csvs <- function(anndata, dirname, skip_data = TRUE, sep = ",") {
		sep = sep
		)))
		}
Original file line number	Diff line number	Diff line change
Expand Up		@@ -38,4 +38,3 @@ write_h5ad <- function(anndata, filename, compression = NULL, compression_opts =
		as_dense = as_dense
		)))
		}