Fix r cmd check warnings

microbiome · Apr 19, 2024 · 143f246 · 143f246
1 parent f998faa
commit 143f246
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Showing 15 changed files with 51 additions and 50 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,3 +3,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+.github
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,7 +21,8 @@ Imports:
     methods,
     S4Vectors
 Suggests:
-    mia
+    mia,
+    vegan
 URL: https://github.com/RiboRings/iSEEtree
 BugReports: https://github.com/RiboRings/iSEEtree/issues
 Roxygen: list(markdown = TRUE)

diff --git a/R/class-AbundanceDensityPlot.R b/R/class-AbundanceDensityPlot.R
@@ -27,9 +27,9 @@
 #' tse <- GlobalPatterns
 #' 
 #' # Agglomerate TreeSE by Genus
-#' tse_genus <- mergeFeaturesByRank(tse,
-#'                                  rank = "Genus",
-#'                                  onRankOnly = TRUE)
+#' tse_genus <- agglomerateByRank(tse,
+#'                                rank = "Genus",
+#'                                onRankOnly = TRUE)
 #'
 #' # Add relabundance assay
 #' tse_genus <- transformAssay(tse_genus, method = "relabundance")
@@ -39,7 +39,7 @@
 #'   iSEE(tse_genus)
 #' }
 #'
-#' @name AbundanceDensityPlot-class
+#' @name AbundanceDensityPlot
 NULL
 
 #' @export

diff --git a/R/class-AbundancePlot.R b/R/class-AbundancePlot.R
@@ -26,16 +26,16 @@
 #' tse <- GlobalPatterns
 #' 
 #' # Agglomerate TreeSE by Genus
-#' tse_genus <- mergeFeaturesByRank(tse,
-#'                                  rank = "Genus",
-#'                                  onRankOnly = TRUE)
+#' tse_genus <- agglomerateByRank(tse,
+#'                                rank = "Genus",
+#'                                onRankOnly = TRUE)
 #'
 #' # Launch iSEE
 #' if (interactive()) {
 #'   iSEE(tse_genus)
 #' }
 #'
-#' @name AbundancePlot-class
+#' @name AbundancePlot
 NULL
 
 #' @export

diff --git a/R/class-RDAPlot.R b/R/class-RDAPlot.R
@@ -41,7 +41,7 @@
 #'   iSEE(tse, initial = c(RDAPlot()))
 #' }
 #' 
-#' @name RDAPlot-class
+#' @name RDAPlot
 NULL
 
 setClassUnion("charlog", c("character", "logical"))

diff --git a/R/class-RowTreePlot.R b/R/class-RowTreePlot.R
@@ -34,16 +34,16 @@
 #' tse <- GlobalPatterns
 #' 
 #' # Agglomerate TreeSE by Genus
-#' tse_genus <- mergeFeaturesByRank(tse,
-#'                                  rank = "Genus",
-#'                                  onRankOnly = TRUE)
+#' tse_genus <- agglomerateByRank(tse,
+#'                                rank = "Genus",
+#'                                onRankOnly = TRUE)
 #'
 #' # Launch iSEE
 #' if (interactive()) {
 #'   iSEE(tse_genus)
 #' }
 #'
-#' @name RowTreePlot-class
+#' @name RowTreePlot
 NULL
 
 #' @export

diff --git a/R/iSEE-default.R b/R/iSEE-default.R
@@ -22,9 +22,9 @@
 #' tse <- GlobalPatterns
 #'
 #' # Agglomerate TreeSE by Genus
-#' tse_genus <- mergeFeaturesByRank(tse,
-#'                                  rank = "Genus",
-#'                                  onRankOnly = TRUE)
+#' tse_genus <- agglomerateByRank(tse,
+#'                                rank = "Genus",
+#'                                onRankOnly = TRUE)
 #'
 #' # Add relabundance assay
 #' tse_genus <- transformAssay(tse_genus, method = "relabundance")
@@ -34,7 +34,7 @@
 #'   iSEE(tse_genus, initial = c(RowTreePlot(), AbundancePlot(), AbundanceDensityPlot()))
 #' }
 #' 
-#' @name iSEE-TreeSE
+#' @name iSEE
 NULL
 
 #' @export

diff --git a/R/iSEEtree-package.R b/R/iSEEtree-package.R
@@ -6,7 +6,7 @@
 #'
 #' @author Giulio Benedetti \email{giulio.benedetti@@utu.fi}
 #'
-#' @name iSEEtree-pkg
+#' @name iSEEtree
 #' @docType package
 #' @keywords internal
 #'

diff --git a/man/AbundanceDensityPlot-class.Rd → man/AbundanceDensityPlot.Rd b/man/AbundanceDensityPlot-class.Rd → man/AbundanceDensityPlot.Rd
diff --git a/man/AbundancePlot-class.Rd → man/AbundancePlot.Rd b/man/AbundancePlot-class.Rd → man/AbundancePlot.Rd
diff --git a/man/RDAPlot-class.Rd → man/RDAPlot.Rd b/man/RDAPlot-class.Rd → man/RDAPlot.Rd
diff --git a/man/RowTreePlot-class.Rd → man/RowTreePlot.Rd b/man/RowTreePlot-class.Rd → man/RowTreePlot.Rd
diff --git a/man/iSEE-TreeSE.Rd → man/iSEE.Rd b/man/iSEE-TreeSE.Rd → man/iSEE.Rd
diff --git a/man/iSEEtree-pkg.Rd → man/iSEEtree.Rd b/man/iSEEtree-pkg.Rd → man/iSEEtree.Rd
diff --git a/_pkgdown.yml → pkgdown/_pkgdown.yml b/_pkgdown.yml → pkgdown/_pkgdown.yml
@@ -2,14 +2,14 @@ destination: docs
 reference:
 - title: Panels
 - contents:
-  - AbundanceDensityPlot-class
-  - AbundancePlot-class
-  - RDAPlot-class
-  - RowTreePlot-class
+  - AbundanceDensityPlot
+  - AbundancePlot
+  - RDAPlot
+  - RowTreePlot
 - title: Other
 - subtitle: Default layout
 - contents:
-  - iSEE-TreeSE
+  - iSEE
 - subtitle: Package
 - contents:
-  - iSEEtree-pkg
+  - iSEEtree
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,3 +3,4 @@ @@
     ^_pkgdown\.yml$
     ^docs$
     ^pkgdown$
+    .github