Simplify reference

R/class-AbundanceDensityPlot.R

@@ -43,12 +43,10 @@
 #' }
 #' 
 #' @docType methods
-#' @aliases AbundanceDensityPlot-class
-#'   initialize,AbundanceDensityPlot-method
-#'
 #' @name AbundanceDensityPlot
 NULL
 
+#' @rdname AbundanceDensityPlot
 #' @export
 setClass("AbundanceDensityPlot", contains="Panel", slots=c(layout="character",
     assay.type="character", n="numeric", dots_colour="character",

R/class-AbundancePlot.R

@@ -38,12 +38,10 @@
 #' }
 #' 
 #' @docType methods
-#' @aliases AbundancePlot-class
-#'   initialize,AbundancePlot-method
-#'
 #' @name AbundancePlot
 NULL
 
+#' @rdname AbundancePlot
 #' @export
 setClass("AbundancePlot", contains="Panel",
     slots=c(rank="character", use_relative="logical", add_legend="logical",

R/class-RDAPlot.R

@@ -60,15 +60,13 @@
 #'   iSEE(tse, initial = c(panel))
 #' }
 #' 
-#' #' @docType methods
-#' @aliases RDAPlot-class
-#'   initialize,RDAPlot-method
-#'
+#' @docType methods
 #' @name RDAPlot
 NULL
 
 setClassUnion("charlog", c("character", "logical"))
 
+#' @rdname RDAPlot
 #' @export
 setClass("RDAPlot", contains="Panel", slots=c(dimred="character",
     add.ellipse="charlog", colour_by="character", vec.text="logical",

R/class-RowTreePlot.R

@@ -57,12 +57,10 @@
 #' }
 #' 
 #' @docType methods
-#' @aliases RowTreePlot-class
-#'   initialize,RowTreePlot-method
-#'
 #' @name RowTreePlot
 NULL
 
+#' @rdname RowTreePlot
 #' @export
 setClass("RowTreePlot", contains="Panel", slots=c(layout="character",
     add_legend="logical", edge_colour_by="character", tip_colour_by="character",

README.md

@@ -20,12 +20,11 @@ in the [iSEE-verse website](https://isee.github.io/) and the
 respectively.
 
 iSEEtree is meant for new and experienced users alike, who desire to create and
-interact with several graphics for microbiome data, without an in-depth
-knowledge of the underlying mia functionality. Current microbiome-specific
-panels include phylogenetic trees, ordination plots and compositional plots,
-which can be further explored below in this article. Other more generic panels
-are also reused from the iSEE package and can be experimented in
-[this article](https://isee.github.io/iSEE/articles/basic.html).
+interact with several graphics for microbiome data, without the need for an
+in-depth knowledge of the underlying mia functionality. Current
+microbiome-specific panels include phylogenetic trees, ordination plots and compositional plots, which can be further explored below in this article. Other
+more generic panels are also reused from the iSEE package and can be
+experimented in [this article](https://isee.github.io/iSEE/articles/basic.html).
 
 ## Installation instructions
 The release version of iSEEtree can be installed from Bioconductor as follows: