pull

Merge branch 'master' of github.com:stemangiola/tidyseurat

Conflicts:
	tests/testthat/test-dplyr.R

.github/workflows/rworkflows.yml

@@ -0,0 +1,57 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidyseurat
 Title: Brings Seurat to the Tidyverse 
-Version: 0.7.2
+Version: 0.7.8
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")),
             person("Maria", "Doyle", email = "[email protected]",
@@ -15,7 +15,7 @@ Depends:
     ttservice (>= 0.3.8),
     SeuratObject
 Imports:
-    Seurat,
+    Seurat (>= 4.3.0),
     tibble,
     dplyr,
     magrittr,

NAMESPACE

@@ -54,6 +54,7 @@ exportMethods(aggregate_cells)
 exportMethods(join_features)
 importFrom(Matrix,rowSums)
 importFrom(Seurat,Assays)
+importFrom(Seurat,DietSeurat)
 importFrom(Seurat,GetAssayData)
 importFrom(Seurat,SplitObject)
 importFrom(Seurat,VariableFeatures)

R/dplyr_methods.R

@@ -12,13 +12,23 @@
 #' @importFrom dplyr arrange
 #' @export
 arrange.Seurat <- function(.data, ..., .by_group=FALSE) {
-    .data@meta.data <-
-        .data %>%
-        as_tibble() %>%
-        dplyr::arrange(  ..., .by_group=.by_group  ) %>%
-        as_meta_data(.data)
-
-    .data
+
+  # DEPRECATE
+  deprecate_warn(
+    when="0.7.5",
+    what="arrange()",
+    details="tidyseurat says: arrange() is temporarly deprected as it is not clear that Seurat allows reordering of cells."
+  )
+
+    # .cell_ordered <-
+    #     .data %>%
+    #     as_tibble() %>%
+    #     dplyr::arrange(  ..., .by_group=.by_group  ) %>%
+    #    pull(!!c_(.data)$symbol)
+    # 
+    # .data[,.cell_ordered]
+
+  .data
 }
 
 #' @name bind_rows
@@ -48,7 +58,7 @@ bind_rows.Seurat <- function(..., .id=NULL,  add.cell.ids=NULL)
     # slot(object=object[[assay]], name="SCTModel.list")
     # So I have to delete any sample of size 1 if I have calculated SCT
     # if()
-    # GetAssayData(object, slot='SCTModel.list', assay="SCT") %>%
+    # GetAssayData(object, layer='SCTModel.list', assay="SCT") %>%
     #     map(~ [email protected] %>% nrow)
 
     # Check if cell with same name
@@ -269,6 +279,7 @@ mutate.Seurat <- function(.data, ...) {
 #' data(pbmc_small)
 #' pbmc_small |> rename(s_score=nFeature_RNA)
 #'
+#' @importFrom Seurat DietSeurat
 #' @importFrom tidyselect eval_select
 #' @importFrom dplyr rename
 #' @export
@@ -281,7 +292,10 @@ rename.Seurat <- function(.data, ...)
         get_special_columns(.data))
 
     # Small df to be more efficient
-    df <- .data[1, 1] |> as_tibble() 
+    df <- 
+      DietSeurat(.data, features = rownames(.data)[1])[,1]  |>
+      suppressWarnings() |> 
+      as_tibble() 
 
     # What columns we are going to create
     cols_from <- tidyselect::eval_select(expr(c(...)), df) |> names()

R/methods.R

@@ -73,38 +73,39 @@ tidy.Seurat <- function(object){
 setMethod("join_features", "Seurat", function(.data,
     features=NULL, all=FALSE, exclude_zeros=FALSE, shape="long",
     assay=NULL, slot="data", ...) {
-    .data %>%
-        when(
-            # Shape is long
-            shape == "long" ~ (.) %>%
-                left_join(
-                    get_abundance_sc_long(
-                        .data=.data,
-                        features=features,
-                        all=all,
-                        exclude_zeros=exclude_zeros,
-                        assay=assay,
-                        slot=slot,
-                        ...
-                    ),
-                    by=c_(.data)$name
-                ) %>%
-                select(!!c_(.data)$symbol, .feature,
-                    contains(".abundance"), everything()),
-            # Shape if wide
-            ~ (.) %>%
-                left_join(
-                    get_abundance_sc_wide(
-                        .data=.data,
-                        features=features,
-                        all=all,
-                        assay=assay,
-                        slot=slot,
-                        ...
-                    ),
-                    by=c_(.data)$name
-                ) 
-            )
+
+  .feature = NULL
+
+  if(shape == "long")
+    .data |> 
+    left_join(
+      get_abundance_sc_long(
+        .data=.data,
+        features=features,
+        all=all,
+        exclude_zeros=exclude_zeros,
+        assay=assay,
+        slot=slot,
+        ...
+      ),
+      by=c_(.data)$name
+    ) %>%
+    select(!!c_(.data)$symbol, .feature,
+           contains(".abundance"), everything())
+  else
+    .data |> 
+    left_join(
+      get_abundance_sc_wide(
+        .data=.data,
+        features=features,
+        all=all,
+        assay=assay,
+        slot=slot,
+        ...
+      ),
+      by=c_(.data)$name
+    ) 
+
 })
 
 
@@ -126,6 +127,7 @@ setMethod("join_features", "Seurat", function(.data,
 #' @importFrom Matrix rowSums
 #' @importFrom ttservice aggregate_cells
 #' @importFrom SeuratObject DefaultAssay
+#' @importFrom Seurat DietSeurat
 #' @importFrom purrr map_int
 #' @export
 setMethod("aggregate_cells", "Seurat",  function(.data,
@@ -140,7 +142,7 @@ setMethod("aggregate_cells", "Seurat",  function(.data,
     # Subset only wanted assays
     if(!is.null(assays)){
         DefaultAssay(.data) <- assays[1]
-        .data@assays <- .data@assays[assays]
+        .data = .data |> DietSeurat(assays = assays)
     }
 
     .data %>%
@@ -151,17 +153,17 @@ setMethod("aggregate_cells", "Seurat",  function(.data,
                 # Loop over assays
                 map2(.x@assays, names(.x@assays),
                     # Get counts
-                    ~ GetAssayData(.x, slot=slot) %>%
+                    ~ GetAssayData(.x, layer=slot) %>%
                         aggregation_function(na.rm=T) %>%
                         tibble::enframe(
                             name=".feature",
                             value=sprintf("%s", .y)
                         ) %>%
                         mutate(.feature=as.character(.feature)) 
                 ) %>%
-                Reduce(function(...) full_join(..., by=c(".feature")), .)            
-            )
-        ) %>%
+                Reduce(function(...) full_join(..., by=c(".feature")), .), 
+                .progress = TRUE          
+        )) %>%
         left_join(
             .data %>%
                 as_tibble() %>%

R/plotly_methods.R

@@ -4,7 +4,8 @@
 #' @return `plotly`
 #' 
 #' @examples
-#' # TODO
+#' data(pbmc_small)
+#' plot_ly(pbmc_small)
 #' 
 #' @importFrom plotly plot_ly
 #' @export

R/tidyr_methods.R

@@ -92,6 +92,7 @@ unnest_seurat  <-  function(data, cols, ...,
 #' @importFrom magrittr equals
 #' @importFrom rlang enquos
 #' @importFrom Seurat SplitObject
+#' @importFrom Seurat DietSeurat
 #' @importFrom rlang :=
 #' @export
 nest.Seurat <- function (.data, ..., .names_sep=NULL)
@@ -106,11 +107,13 @@ nest.Seurat <- function (.data, ..., .names_sep=NULL)
         .data <- ping_old_special_column_into_metadata(.data)
     }
 
-    my_data__ <- .data
+    my_data__ <- .data 
 
     # This is for getting the column names
     dummy_nested <- 
-        my_data__[1,] |>
+        my_data__ |> 
+        DietSeurat(features = rownames(my_data__)[1:2], assays = DefaultAssay(my_data__)) |>
+        suppressWarnings() |> 
         to_tib() %>%
         tidyr::nest(...)