Add Rworkflows (#85)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>

.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: devel
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: devel
+          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

@@ -24,7 +24,8 @@ Imports:
     S4Vectors,
     SummarizedExperiment,
     SingleCellExperiment,
-    vegan
+    vegan,
+    scater
 Suggests: 
     TreeSummarizedExperiment,
     tidySingleCellExperiment,
@@ -41,7 +42,7 @@ Suggests:
 Encoding: UTF-8
 URL: https://github.com/microbiome/miaTime
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 LazyData: false
 Config/testthat/edition: 3

vignettes/articles/manipulation.Rmd

@@ -71,7 +71,7 @@ The _tidySingleCellExperiment_ package provides handy functions for (Tree)SE man
 library("tidySingleCellExperiment")
 data(hitchip1006)
 tse <- hitchip1006
-tse2 <- tse %>% tidySingleCellExperiment::arrange(subject, time)
+tse2 <- tse %>% arrange(subject, time)
 ```
 
 

vignettes/articles/minimalgut.Rmd

@@ -88,7 +88,7 @@ tse <- getBaselineDivergence(tse,
                              time_field = "Time.hr",
                              name_divergence = "divergence_from_baseline",
                              name_timedifference = "time_from_baseline",
-                             assay_name="relabundance",
+                             assay.type="relabundance",
                              FUN = vegan::vegdist,
                              method="bray")
 
@@ -128,7 +128,7 @@ plotSeries(mia::relAbundanceCounts(minimalgut),
            x = "Time.hr",
            y = "Blautia_hydrogenotrophica",
            colour_by = "Species",
-           assay_name = "relabundance")+
+           assay.type = "relabundance")+
     geom_vline(xintercept = 152, lty=2, color="#991720") + 
     geom_vline(xintercept = 248, lty=2, color= "#0963bd")+
     annotate("text",x=c(152, 248),y=c(0.2, 0.15),
@@ -160,7 +160,7 @@ tse <- getStepwiseDivergence(tse, group = "StudyIdentifier",
                                time_field = "Time_hr_num",
                                name_divergence = "divergence_from_previous_step",
                                name_timedifference = "time_from_previous_step",
-                               assay_name="relabundance",
+                               assay.type ="relabundance",
                                FUN = vegan::vegdist,
                                method="bray")