Dev

.github/workflows/check-bioc.yml

@@ -39,6 +39,7 @@ env:
   run_pkgdown: 'true'
   has_RUnit: 'false'
   cache-version: 'cache-v1'
+  run_docker: 'false'
 
 jobs:
   build-check:
@@ -51,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.0', bioc: '3.12', cont: "bioconductor/bioconductor_docker:RELEASE_3_12", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.0', bioc: '3.12'}
-          - { os: windows-latest, r: '4.0', bioc: '3.12'}
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.13', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.13'}
+          - { os: windows-latest, r: 'devel', bioc: '3.13'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -101,16 +102,16 @@ jobs:
         uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v2
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -156,6 +157,13 @@ jobs:
         run: |
           BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
         shell: Rscript {0}
+
+      ## 12th April 2021 No Seurat binary available for Mac currently so install from source
+      - name: Install Seurat for macOS-latest
+        if: matrix.config.os == 'macOS-latest'
+        run: |
+          BiocManager::install("Seurat", type="source")
+        shell: Rscript {0}
 
       - name: Install dependencies pass 1
         run: |
@@ -180,7 +188,7 @@ jobs:
           ## Pass #2 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
-          
+
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
           remotes::install_cran("rcmdcheck")
@@ -203,7 +211,7 @@ jobs:
       - name: Install pkgdown
         if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
-          remotes::install_cran("pkgdown")
+          remotes::install_github("r-lib/pkgdown")
         shell: Rscript {0}
 
       - name: Session info
@@ -272,6 +280,15 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-results
+          name: ${{ runner.os }}-biocversion-devel-r-devel-results
           path: check
-
+
+      - uses: docker/build-push-action@v1
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+          repository: stemangiola/tidybulk
+          tag_with_ref: true
+          tag_with_sha: true
+          tags: latest

DESCRIPTION

@@ -66,7 +66,8 @@ Suggests:
     devtools,
     functional,
     survminer,
-    tidySummarizedExperiment
+    tidySummarizedExperiment,
+    markdown
 VignetteBuilder: 
     knitr
 RdMacros:
@@ -76,3 +77,4 @@ biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpr
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.1
+LazyDataCompression: xz

NAMESPACE

@@ -81,6 +81,7 @@ import(tibble)
 import(tidyr)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
+importFrom(SummarizedExperiment,rowData)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,distinct)
@@ -151,6 +152,7 @@ importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_split)
 importFrom(tibble,as_tibble)
+importFrom(tibble,enframe)
 importFrom(tibble,tibble)
 importFrom(tidyr,complete)
 importFrom(tidyr,nest)

R/data.R

@@ -1,13 +1,3 @@
-#' Example data set
-#'
-#'
-"counts"
-
-#' Example data set reduced
-#'
-#'
-"counts_mini"
-
 #' Cibersort reference
 #'
 #'
@@ -23,11 +13,6 @@
 #'
 "ensembl_symbol_mapping"
 
-#' Data set
-#'
-#'
-"breast_tcga_mini"
-
 #' flybaseIDs
 #'
 #'

R/dplyr_methods.R

@@ -201,7 +201,7 @@ bind_cols.tidybulk <- function(..., .id = NULL)
 #' 
 #' @examples
 #'
-#' distinct(tidybulk::counts_mini)
+#' tidybulk::se_mini %>% tidybulk() %>% distinct()
 #'
 #'
 #' @export
@@ -723,8 +723,8 @@ rowwise.tidybulk <- function(data, ...)
 #'
 #' @examples
 #'`%>%` = magrittr::`%>%`
-#' annotation = tidybulk::counts %>% distinct(sample) %>% mutate(source = "AU")
-#' tidybulk::counts %>% left_join(annotation)
+#' annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble() %>% distinct(sample) %>% mutate(source = "AU")
+#' tidybulk::counts_SE %>% tidybulk() %>% as_tibble() %>% left_join(annotation)
 #'
 #' @rdname dplyr-methods
 #' @name left_join
@@ -763,8 +763,8 @@ left_join.tidybulk <- function (x, y, by = NULL, copy = FALSE, suffix = c(".x",
 #'
 #' @examples
 #'`%>%` = magrittr::`%>%`
-#' annotation = tidybulk::counts %>% distinct(sample) %>% mutate(source = "AU")
-#' tidybulk::counts %>% inner_join(annotation)
+#' annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble() %>% distinct(sample) %>% mutate(source = "AU")
+#' tidybulk::counts_SE %>% tidybulk() %>% as_tibble() %>% inner_join(annotation)
 #'
 #' @rdname join-methods
 #' @name inner_join
@@ -802,8 +802,8 @@ inner_join.tidybulk <- function (x, y, by = NULL, copy = FALSE, suffix = c(".x",
 #'
 #' @examples
 #'`%>%` = magrittr::`%>%`
-#' annotation = tidybulk::counts %>% distinct(sample) %>% mutate(source = "AU")
-#' tidybulk::counts %>% right_join(annotation)
+#' annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble() %>% distinct(sample) %>% mutate(source = "AU")
+#' tidybulk::counts_SE %>% tidybulk() %>% as_tibble() %>% right_join(annotation)
 #'
 #' @rdname join-methods
 #' @name right_join
@@ -843,8 +843,8 @@ right_join.tidybulk <- function (x, y, by = NULL, copy = FALSE, suffix = c(".x",
 #'
 #' @examples
 #'`%>%` = magrittr::`%>%`
-#' annotation = tidybulk::counts %>% distinct(sample) %>% mutate(source = "AU")
-#' tidybulk::counts %>% full_join(annotation)
+#' annotation = tidybulk::counts_SE %>% tidybulk() %>% as_tibble() %>% distinct(sample) %>% mutate(source = "AU")
+#' tidybulk::counts_SE %>% tidybulk() %>% as_tibble() %>% full_join(annotation)
 #'
 #' @rdname join-methods
 #' @name full_join