plotOrdination, plotJointRPCA and modification to plotRDA

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: miaViz
 Title: Microbiome Analysis Plotting and Visualization
-Version: 1.21.1
+Version: 1.21.2
 Authors@R: 
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "tuomas.v.borman@utu.fi",
@@ -31,7 +31,7 @@ License: Artistic-2.0 | file LICENSE
 Encoding: UTF-8
 LazyData: false
 Depends:
-    R (>= 4.0),
+    R (>= 4.1),
     ggplot2,
     ggraph (>= 2.0),
     mia (>= 1.13.0),
@@ -47,6 +47,7 @@ Imports:
     ggnewscale,
     ggrepel,
     ggtree,
+    grid,
     methods,
     patchwork,
     rlang,

NAMESPACE

@@ -10,9 +10,11 @@ export(plotDMNFit)
 export(plotFeaturePrevalence)
 export(plotForest)
 export(plotHistogram)
+export(plotJointRPCA)
 export(plotLoadings)
 export(plotMediation)
 export(plotNMDS)
+export(plotOrdination)
 export(plotPrevalence)
 export(plotPrevalentAbundance)
 export(plotRDA)
@@ -39,8 +41,10 @@ exportMethods(plotDMNFit)
 exportMethods(plotFeaturePrevalence)
 exportMethods(plotForest)
 exportMethods(plotHistogram)
+exportMethods(plotJointRPCA)
 exportMethods(plotLoadings)
 exportMethods(plotMediation)
+exportMethods(plotOrdination)
 exportMethods(plotPrevalence)
 exportMethods(plotPrevalentAbundance)
 exportMethods(plotRDA)
@@ -80,6 +84,7 @@ importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(TreeSummarizedExperiment,colTree)
 importFrom(TreeSummarizedExperiment,colTreeNames)
+importFrom(TreeSummarizedExperiment,rowLinks)
 importFrom(TreeSummarizedExperiment,rowTree)
 importFrom(TreeSummarizedExperiment,rowTreeNames)
 importFrom(ape,as.phylo)
@@ -106,6 +111,7 @@ importFrom(dplyr,rename)
 importFrom(dplyr,rename_with)
 importFrom(dplyr,row_number)
 importFrom(dplyr,select)
+importFrom(dplyr,slice_max)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
@@ -147,8 +153,6 @@ importFrom(ggplot2,scale_y_discrete)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_classic)
-importFrom(ggplot2,xlab)
-importFrom(ggplot2,ylab)
 importFrom(ggrepel,geom_label_repel)
 importFrom(ggrepel,geom_text_repel)
 importFrom(ggtree,geom_cladelab)
@@ -162,6 +166,8 @@ importFrom(ggtree,ggtree)
 importFrom(ggtree,gheatmap)
 importFrom(ggtree,groupOTU)
 importFrom(ggtree,theme_tree)
+importFrom(grid,arrow)
+importFrom(grid,unit)
 importFrom(mia,meltSE)
 importFrom(patchwork,plot_layout)
 importFrom(patchwork,wrap_plots)
@@ -170,7 +176,6 @@ importFrom(rlang,":=")
 importFrom(rlang,sym)
 importFrom(scales,pretty_breaks)
 importFrom(scales,rescale)
-importFrom(scater,plotReducedDim)
 importFrom(scater,retrieveCellInfo)
 importFrom(scater,retrieveFeatureInfo)
 importFrom(stats,formula)

NEWS

@@ -51,3 +51,6 @@ Changes in version 1.17.x
 Changes in version 1.19.x
 + plotRDA: Now plotting works with interaction term (2025-11-09)
 + plotBoxplot: Added option to add p-values (2026-01-07)
+
+Changes in version 1.21.x
++ Added plotOrdination and plotJointRPCA (2026-08-04)

R/AllGenerics.R

@@ -156,3 +156,13 @@ setGeneric("plotBarplot", signature = c("x"), function(x, ...)
 #' @export
 setGeneric("plotBoxplot", signature = c("object"), function(object, ...)
     standardGeneric("plotBoxplot"))
+
+#' @rdname plotOrdination
+#' @export
+setGeneric("plotOrdination", signature = c("x"), function(x, ...)
+    standardGeneric("plotOrdination"))
+
+#' @rdname plotJointRPCA
+#' @export
+setGeneric("plotJointRPCA", signature = c("x"), function(x, ...)
+    standardGeneric("plotJointRPCA"))

R/plotBoxplot.R

@@ -1106,14 +1106,16 @@ setMethod("plotBoxplot", signature = c(object = "SummarizedExperiment"),
 
 # This function adds points to plot
 .add_points_layer <- function(
-        p, df, point.alpha = 0.65, point.size = 2, point.shape = 19L,
+        p, df,
+        x = NULL, y = NULL,
+        point.alpha = 0.65, point.size = 2, point.shape = 19L,
         point.colour = point.color, point.color = "grey70", ...){
     # To disable "no visible binding for global variable" message in cmdcheck
     x_point <- y_point <- NULL
     args <- list(
         mapping = aes(
-            x = x_point,
-            y = y_point,
+            x = if(!is.null(x)) .data[[x]] else x_point,
+            y = if(!is.null(y)) .data[[y]] else  y_point,
             colour = if(!is.null(attributes(df)[["colour.by"]]))
                 .data[[attributes(df)[["colour.by"]]]],
             shape = if(!is.null(attributes(df)[["shape.by"]]))
@@ -1332,5 +1334,22 @@ setMethod("plotBoxplot", signature = c(object = "SummarizedExperiment"),
     if( !is.null(attributes(df)[["size.by"]]) ){
         p <- p + labs(shape = attributes(df)[["size.by"]])
     }
+
+    # Adjust colors
+    if( !is.null(attributes(df)[["colour.by"]]) ){
+        name <- attributes(df)[["colour.by"]]
+        vals <- df[[name]]
+        p <- .resolve_plot_colours(
+            p, vals, name,
+        )
+    }
+    if( !is.null(attributes(df)[["fill.by"]]) ){
+        name <- attributes(df)[["fill.by"]]
+        vals <- df[[name]]
+        p <- .resolve_plot_colours(
+            p, vals, name, fill = TRUE
+        )
+    }
+
     return(p)
 }