Fix docs

Author: RiboRings

R/class-AbundanceDensityPlot.R

@@ -15,7 +15,8 @@
 #' \item \code{order_descending}, a string specifying the descending order.
 #' }
 #'
-#' In addition, this class inherits all slots from its parent \linkS4class{Panel} class.
+#' In addition, this class inherits all slots from its parent class
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #'
 #' @return
 #' The \code{AbundanceDensityPlot(...)} constructor creates an instance of an

R/class-AbundancePlot.R

@@ -13,7 +13,8 @@
 #' \item \code{add_legend}, a logical indicating if the color legend should appear.
 #' }
 #'
-#' In addition, this class inherits all slots from its parent \linkS4class{Panel} class.
+#' In addition, this class inherits all slots from its parent class
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #'
 #' @return
 #' The \code{AbundancePlot(...)} constructor creates an instance of an

R/class-LoadingPlot.R

@@ -14,7 +14,8 @@
 #' \item \code{add.tree}, a logical indicating whether the tree should be shown.
 #' }
 #'
-#' In addition, this class inherits all slots from its parent \linkS4class{Panel} class.
+#' In addition, this class inherits all slots from its parent class
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #'
 #' @return
 #' The \code{LoadingPlot(...)} constructor creates an instance of an

R/class-RDAPlot.R

@@ -30,7 +30,8 @@
 #'  on the coordinate axes.
 #' }
 #'
-#' In addition, this class inherits all slots from its parent \linkS4class{Panel} class.
+#' In addition, this class inherits all slots from its parent class
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #'
 #' @return
 #' The \code{RDAPlot(...)} constructor creates an instance of a RDAPlot class,

R/class-ScreePlot.R

@@ -45,8 +45,8 @@
 #'   (Default: \code{c("eig", "varExplained")})
 #' }
 #' 
-#' In addition, this class inherits all slots from its parent
-#' \linkS4class{Panel} class.
+#' In addition, this class inherits all slots from its parent class
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #'
 #' @return
 #' The \code{ScreePlot(...)} constructor creates an instance of an ScreePlot

R/family-GraphPlot.R

@@ -35,7 +35,7 @@
 #' }
 #'
 #' In addition, this class inherits all slots from its parent class
-#' \linkS4class{Panel}.
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #' 
 #' @seealso
 #' \linkS4class{RowGraphPlot}

R/family-TreePlot.R

@@ -41,7 +41,7 @@
 #' }
 #'
 #' In addition, this class inherits all slots from its parent
-#' \linkS4class{Panel} class.
+#' \code{\link[iSEE:Panel-class]{Panel}}.
 #' 
 #' @seealso
 #' \linkS4class{RowTreePlot}

R/iSEEtree-package.R

@@ -1,6 +1,6 @@
 #' iSEE extension for the TreeSummarizedExperiment container
 #'
-#' `iSEEtree` is an extension of \pkg{iSEE} that provides panels for the
+#' \code{iSEEtree} is an extension of \pkg{iSEE} that provides panels for the
 #' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-constructor]{TreeSummarizedExperiment}}
 #' container, enabling the interactive visualisation of typical microbiome data.
 #' The panel layout of iSEEtree is described in \code{\link{iSEE}}.
@@ -14,6 +14,6 @@
 #' 
 #' @docType package
 #' @keywords internal
-#' @name iSEEtree
+#' @name iSEEtree-package
 #' 
 "_PACKAGE"

R/utils.R

@@ -29,6 +29,7 @@
 #' # View filtered list of panels
 #' initial
 #' 
+#' @keywords internal
 #' @name utils
 NULL
 

man/AbundanceDensityPlot.Rd

@@ -31,4 +31,4 @@ reference:
   - utils
 - subtitle: Package
 - contents:
-  - iSEEtree
+  - iSEEtree-package