Start using rworkflows, minor fixes

.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

@@ -1,6 +1,6 @@
 Package: miaViz
 Title: Microbiome Analysis Plotting and Visualization
-Version: 1.11.2
+Version: 1.11.3
 Authors@R: 
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",
@@ -61,6 +61,8 @@ Suggests:
     vegan,
     microbiomeDataSets,
     bluster
+Remotes:
+    github::microbiome/miaTime
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 VignetteBuilder: knitr

R/plotCCA.R

@@ -51,7 +51,7 @@
 #' @param label.color Alias for `label.colour`.
 #' 
 #' @param sep.group String specifying the separator used in the labels.
-#'   (default: \code{sep.group = "\U2012"})
+#'   (default: \code{sep.group = "\U2014"})
 #'   
 #' @param repl.underscore String used to replace underscores in the labels.
 #'   (default: \code{repl.underscore = " "})
@@ -182,7 +182,7 @@ setMethod("plotRDA", signature = c(object = "SingleCellExperiment"),
              add.ellipse = TRUE, ellipse.alpha = 0.2, ellipse.linewidth = 0.1, ellipse.linetype = 1,
              vec.size = 0.5, vec.color = vec.colour, vec.colour = "black", vec.linetype = 1,
              arrow.size = 0.25, label.color = label.colour, label.colour = "black", label.size = 4,
-             vec.text = TRUE, repel.labels = TRUE, sep.group = "\U2012", repl.underscore = " ",
+             vec.text = TRUE, repel.labels = TRUE, sep.group = "\U2014", repl.underscore = " ",
              add.significance = TRUE, add.expl.var = TRUE, add.vectors = TRUE, parse.labels = TRUE, ...){
         ###################### Input check ########################
         if( !(add.ellipse %in% c(TRUE, FALSE, "fill", "color", "colour")) ){
@@ -441,7 +441,7 @@ setMethod("plotRDA", signature = c(object = "matrix"),
 # Make vector labels more tidy, i.e, separate variable and group names.
 # Replace also underscores with space
 .tidy_vector_labels <- function(
-        vector_label, coldata, sep.group = "\U2012", repl.underscore = " ", ...){
+        vector_label, coldata, sep.group = "\U2014", repl.underscore = " ", ...){
     # Get variable names from sample metadata
     var_names <- colnames(coldata)
     # Loop through vector labels