Add plotNMDS to miaViz

NAMESPACE

@@ -6,6 +6,7 @@ export(plotColGraph)
 export(plotColTile)
 export(plotDMNFit)
 export(plotFeaturePrevalence)
+export(plotNMDS)
 export(plotPrevalence)
 export(plotPrevalentAbundance)
 export(plotRDA)

NEWS

@@ -28,3 +28,4 @@ Changes in version 1.11.x
 Changes in version 1.13.x
 + plot*Tree: bugfix, ununique nodes
 + Added confidence.level parameter to plotCCA
++ add plotNMDS to miaViz (plotNMDS deprecated in mia)

R/plotNDMS.R

@@ -0,0 +1,21 @@
+#' Wrapper for scater::plotReducedDim()
+#' 
+#' @param x a
+#'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
+#'   object.
+#'   
+#' @param ncomponents 	
+#'   A numeric scalar indicating the number of dimensions to plot, starting from 
+#'   the first dimension. Alternatively, a numeric vector specifying the 
+#'   dimensions to be plotted. (Default: 2)
+#'   
+#' @param ... additional arguments passed to scater::plotReducedDim().
+#'   
+#' @name plotNMDS
+NULL
+
+#' @rdname plotNMDS
+#' @export
+plotNMDS <- function(x, ..., ncomponents = 2){
+    plotReducedDim(x, ncomponents = ncomponents, dimred = "NMDS", ...)
+}

tests/testthat/test-plotNMDS.R

@@ -0,0 +1,7 @@
+test_that("plotNMDS", {
+    # Test the class of plotNMDS output
+    data("esophagus", package = "mia")
+    esophagus <- runNMDS(esophagus)
+    plot <- plotNMDS(esophagus)
+    expect_s3_class(plot,c("gg","ggplot"))
+})