Add multimedia example datasets (se_relative, tse_relative)

DESCRIPTION

@@ -82,7 +82,7 @@ Suggests:
     vegan,
     vipor
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 URL: https://github.com/microbiome/miaViz
 BugReports: https://github.com/microbiome/miaViz/issues
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -63,147 +63,195 @@ import(ggplot2)
 import(ggraph)
 import(methods)
 import(mia)
-importFrom(BiocGenerics,ncol)
-importFrom(BiocGenerics,nrow)
-importFrom(BiocParallel,SerialParam)
-importFrom(BiocParallel,bpisup)
-importFrom(BiocParallel,bplapply)
-importFrom(BiocParallel,bpmapply)
-importFrom(BiocParallel,bpstart)
-importFrom(BiocParallel,bpstop)
-importFrom(DelayedArray,rowMeans)
-importFrom(DelayedArray,rowSums)
+importFrom(BiocGenerics,
+  ncol,
+  nrow
+)
+importFrom(BiocParallel,
+  SerialParam,
+  bpisup,
+  bplapply,
+  bpmapply,
+  bpstart,
+  bpstop
+)
+importFrom(DelayedArray,
+  rowMeans,
+  rowSums
+)
 importFrom(DirichletMultinomial,mixture)
-importFrom(S4Vectors,metadata)
-importFrom(S4Vectors,unfactor)
-importFrom(SingleCellExperiment,reducedDim)
-importFrom(SingleCellExperiment,reducedDimNames)
-importFrom(SingleCellExperiment,reducedDims)
-importFrom(SummarizedExperiment,"rowData<-")
-importFrom(SummarizedExperiment,assay)
-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)
-importFrom(ape,drop.tip)
-importFrom(ape,keep.tip)
-importFrom(ape,rotateConstr)
-importFrom(dplyr,"%>%")
-importFrom(dplyr,across)
-importFrom(dplyr,all_of)
-importFrom(dplyr,arrange)
-importFrom(dplyr,case_when)
-importFrom(dplyr,desc)
-importFrom(dplyr,distinct)
-importFrom(dplyr,filter)
-importFrom(dplyr,group_by)
-importFrom(dplyr,group_modify)
-importFrom(dplyr,last_col)
-importFrom(dplyr,mutate)
-importFrom(dplyr,n)
-importFrom(dplyr,n_distinct)
-importFrom(dplyr,pull)
-importFrom(dplyr,relocate)
-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)
-importFrom(ggnewscale,new_scale)
-importFrom(ggnewscale,new_scale_colour)
-importFrom(ggnewscale,new_scale_fill)
-importFrom(ggplot2,aes)
-importFrom(ggplot2,annotate)
-importFrom(ggplot2,coord_cartesian)
-importFrom(ggplot2,coord_flip)
-importFrom(ggplot2,element_blank)
-importFrom(ggplot2,element_rect)
-importFrom(ggplot2,element_text)
-importFrom(ggplot2,expansion)
-importFrom(ggplot2,facet_grid)
-importFrom(ggplot2,facet_wrap)
-importFrom(ggplot2,geom_bar)
-importFrom(ggplot2,geom_errorbar)
-importFrom(ggplot2,geom_line)
-importFrom(ggplot2,geom_point)
-importFrom(ggplot2,geom_raster)
-importFrom(ggplot2,geom_segment)
-importFrom(ggplot2,geom_text)
-importFrom(ggplot2,geom_tile)
-importFrom(ggplot2,geom_vline)
-importFrom(ggplot2,ggplot)
-importFrom(ggplot2,ggplot_build)
-importFrom(ggplot2,labs)
-importFrom(ggplot2,position_dodge)
-importFrom(ggplot2,position_dodge2)
-importFrom(ggplot2,scale_colour_manual)
-importFrom(ggplot2,scale_fill_distiller)
-importFrom(ggplot2,scale_fill_gradient2)
-importFrom(ggplot2,scale_fill_manual)
-importFrom(ggplot2,scale_fill_viridis_d)
-importFrom(ggplot2,scale_size_identity)
-importFrom(ggplot2,scale_x_continuous)
-importFrom(ggplot2,scale_x_discrete)
-importFrom(ggplot2,scale_y_continuous)
-importFrom(ggplot2,scale_y_discrete)
-importFrom(ggplot2,theme)
-importFrom(ggplot2,theme_bw)
-importFrom(ggplot2,theme_classic)
-importFrom(ggplot2,theme_minimal)
-importFrom(ggrepel,geom_label_repel)
-importFrom(ggrepel,geom_text_repel)
-importFrom(ggtree,geom_cladelab)
-importFrom(ggtree,geom_highlight)
-importFrom(ggtree,geom_nodelab)
-importFrom(ggtree,geom_nodepoint)
-importFrom(ggtree,geom_tiplab)
-importFrom(ggtree,geom_tippoint)
-importFrom(ggtree,geom_tree)
-importFrom(ggtree,ggtree)
-importFrom(ggtree,gheatmap)
-importFrom(ggtree,groupOTU)
-importFrom(ggtree,theme_tree)
-importFrom(grid,arrow)
-importFrom(grid,unit)
+importFrom(S4Vectors,
+  metadata,
+  unfactor
+)
+importFrom(SingleCellExperiment,
+  reducedDim,
+  reducedDimNames,
+  reducedDims
+)
+importFrom(SummarizedExperiment,
+  "rowData<-",
+  assay,
+  colData,
+  rowData
+)
+importFrom(TreeSummarizedExperiment,
+  colTree,
+  colTreeNames,
+  rowLinks,
+  rowTree,
+  rowTreeNames
+)
+importFrom(ape,
+  as.phylo,
+  drop.tip,
+  keep.tip,
+  rotateConstr
+)
+importFrom(dplyr,
+  "%>%",
+  across,
+  all_of,
+  arrange,
+  case_when,
+  desc,
+  distinct,
+  filter,
+  group_by,
+  group_modify,
+  last_col,
+  mutate,
+  n,
+  n_distinct,
+  pull,
+  relocate,
+  rename,
+  rename_with,
+  row_number,
+  select,
+  slice_max,
+  summarise,
+  summarize,
+  ungroup
+)
+importFrom(ggnewscale,
+  new_scale,
+  new_scale_colour,
+  new_scale_fill
+)
+importFrom(ggplot2,
+  aes,
+  annotate,
+  coord_cartesian,
+  coord_flip,
+  element_blank,
+  element_rect,
+  element_text,
+  expansion,
+  facet_grid,
+  facet_wrap,
+  geom_bar,
+  geom_errorbar,
+  geom_line,
+  geom_point,
+  geom_raster,
+  geom_segment,
+  geom_text,
+  geom_tile,
+  geom_vline,
+  ggplot,
+  ggplot_build,
+  labs,
+  position_dodge,
+  position_dodge2,
+  scale_colour_manual,
+  scale_fill_distiller,
+  scale_fill_gradient2,
+  scale_fill_manual,
+  scale_fill_viridis_d,
+  scale_size_identity,
+  scale_x_continuous,
+  scale_x_discrete,
+  scale_y_continuous,
+  scale_y_discrete,
+  theme,
+  theme_bw,
+  theme_classic,
+  theme_minimal
+)
+importFrom(ggrepel,
+  geom_label_repel,
+  geom_text_repel
+)
+importFrom(ggtree,
+  geom_cladelab,
+  geom_highlight,
+  geom_nodelab,
+  geom_nodepoint,
+  geom_tiplab,
+  geom_tippoint,
+  geom_tree,
+  ggtree,
+  gheatmap,
+  groupOTU,
+  theme_tree
+)
+importFrom(grid,
+  arrow,
+  unit
+)
 importFrom(mia,meltSE)
-importFrom(patchwork,plot_layout)
-importFrom(patchwork,wrap_plots)
-importFrom(rlang,"!!")
-importFrom(rlang,":=")
-importFrom(rlang,sym)
-importFrom(scales,pretty_breaks)
-importFrom(scales,rescale)
-importFrom(scater,retrieveCellInfo)
-importFrom(scater,retrieveFeatureInfo)
-importFrom(stats,formula)
-importFrom(stats,median)
-importFrom(stats,qt)
-importFrom(stats,runif)
-importFrom(stats,sd)
+importFrom(patchwork,
+  plot_layout,
+  wrap_plots
+)
+importFrom(rlang,
+  "!!",
+  ":=",
+  sym
+)
+importFrom(scales,
+  pretty_breaks,
+  rescale
+)
+importFrom(scater,
+  retrieveCellInfo,
+  retrieveFeatureInfo
+)
+importFrom(stats,
+  formula,
+  median,
+  qt,
+  runif,
+  sd
+)
 importFrom(tibble,rownames_to_column)
-importFrom(tidygraph,activate)
-importFrom(tidygraph,as_tbl_graph)
-importFrom(tidygraph,as_tibble)
-importFrom(tidyr,complete)
-importFrom(tidyr,drop_na)
-importFrom(tidyr,pivot_longer)
-importFrom(tidyr,pivot_wider)
-importFrom(tidytext,reorder_within)
-importFrom(tidytext,scale_y_reordered)
-importFrom(tidytree,as.phylo)
-importFrom(tidytree,as.treedata)
-importFrom(tidytree,as_tibble)
-importFrom(tidytree,child)
-importFrom(tidytree,groupOTU)
-importFrom(tidytree,isTip)
-importFrom(tidytree,rootnode)
+importFrom(tidygraph,
+  activate,
+  as_tbl_graph,
+  as_tibble
+)
+importFrom(tidyr,
+  complete,
+  drop_na,
+  pivot_longer,
+  pivot_wider
+)
+importFrom(tidytext,
+  reorder_within,
+  scale_y_reordered
+)
+importFrom(tidytree,
+  as.phylo,
+  as.treedata,
+  as_tibble,
+  child,
+  groupOTU,
+  isTip,
+  rootnode
+)
 importFrom(utils,getFromNamespace)
-importFrom(viridis,scale_colour_viridis)
-importFrom(viridis,scale_fill_viridis)
+importFrom(viridis,
+  scale_colour_viridis,
+  scale_fill_viridis
+)

NEWS

@@ -55,3 +55,4 @@ Changes in version 1.19.x
 Changes in version 1.21.x
 + Added plotOrdination and plotJointRPCA (2026-08-04)
 + Added plotHeatmap (2026-08-10)
++ Added multimedia_data_demo example datasets (se_relative, tse_relative, tse_pathway) (2026-09-01)