Add plot method for CompositionMatrix

DESCRIPTION

@@ -27,14 +27,14 @@ Imports:
     dimensio (>= 0.4.0),
     graphics,
     grDevices,
+    isopleuros (>= 1.0.0),
     methods,
     MASS,
     stats,
     utils
 Suggests: 
     folio,
     igraph,
-    isopleuros,
     knitr,
     rmarkdown,
     rsvg,

NAMESPACE

@@ -9,6 +9,7 @@ S3method(dist,CompositionMatrix)
 S3method(mahalanobis,CompositionMatrix)
 S3method(mahalanobis,ILR)
 S3method(mean,CompositionMatrix)
+S3method(plot,CompositionMatrix)
 S3method(plot,LogRatio)
 S3method(plot,OutlierIndex)
 export(remove_NA)
@@ -93,3 +94,4 @@ importFrom(stats,var)
 importFrom(utils,combn)
 importFrom(utils,tail)
 importMethodsFrom(dimensio,pca)
+importMethodsFrom(isopleuros,ternary_pairs)

R/AllGenerics.R

@@ -808,6 +808,23 @@ NULL
 #' @rdname barplot
 NULL
 
+#' Plot Compositional Data
+#'
+#' Displays a matrix of ternary plots.
+#' @param x A [`CompositionMatrix-class`] object.
+#' @inheritParams isopleuros::ternary_pairs
+#' @return
+#'  `plot()` is called for its side-effects: is results in a graphic being
+#'  displayed (invisibly return `x`).
+#' @seealso [isopleuros::ternary_pairs()], [isopleuros::ternary_plot()]
+#' @example inst/examples/ex-plot.R
+#' @author N. Frerebeau
+#' @docType methods
+#' @family plot methods
+#' @name plot
+#' @rdname plot
+NULL
+
 #' Plot Log-Ratios
 #'
 #' Displays a density plot.

R/nexus-package.R

@@ -42,6 +42,7 @@
 
 #' @import arkhe
 #' @importMethodsFrom dimensio pca
+#' @importMethodsFrom isopleuros ternary_pairs
 #' @importFrom grDevices hcl.colors
 #' @importFrom methods as as<- callGeneric callNextMethod
 #'  .hasSlot initialize is new setClass setGeneric setMethod slot slot<-

R/plot.R

@@ -3,6 +3,18 @@
 NULL
 
 # CompositionMatrix ============================================================
+#' @export
+#' @method plot CompositionMatrix
+plot.CompositionMatrix <- function(x, ..., margin = NULL) {
+  isopleuros::ternary_pairs(x, margin = margin, ...)
+  invisible(x)
+}
+
+#' @export
+#' @rdname plot
+#' @aliases plot,CompositionMatrix-method
+setMethod("plot", c(x = "CompositionMatrix"), plot.CompositionMatrix)
+
 #' @export
 #' @method barplot CompositionMatrix
 barplot.CompositionMatrix <- function(height, ...,

inst/examples/ex-plot.R

@@ -0,0 +1,6 @@
+## Coerce to compositional data
+data("hongite")
+coda <- as_composition(hongite)
+
+## Ternary plots
+plot(coda)

inst/tinytest/test_plot.R

@@ -9,6 +9,10 @@ if (at_home()) {
   data("hongite")
   coda <- as_composition(hongite)
 
+  # Plot =======================================================================
+  plot_pairs <- function() plot(coda, order = NULL)
+  expect_snapshot_plot(plot_pairs, "plot_pairs")
+
   # Barplot ====================================================================
   plot_barplot <- function() barplot(coda, order = NULL)
   expect_snapshot_plot(plot_barplot, "plot_barplot")