# Generated by roxygen2: do not edit by hand

export(plotAbundanceDensity)
export(plotBarplot)
export(plotBoxplot)
export(plotCCA)
export(plotColGraph)
export(plotColTile)
export(plotDMNFit)
export(plotFeaturePrevalence)
export(plotForest)
export(plotHeatmap)
export(plotHistogram)
export(plotJointRPCA)
export(plotLoadings)
export(plotMediation)
export(plotNMDS)
export(plotOrdination)
export(plotPrevalence)
export(plotPrevalentAbundance)
export(plotRDA)
export(plotRowGraph)
export(plotRowPrevalence)
export(plotRowTile)
export(plotScree)
export(plotSeries)
export(plotTaxaPrevalence)
exportMethods("colTreeData<-")
exportMethods("rowTreeData<-")
exportMethods(colTreeData)
exportMethods(combineTreeData)
exportMethods(getNeatOrder)
exportMethods(plotAbundance)
exportMethods(plotAbundanceDensity)
exportMethods(plotBarplot)
exportMethods(plotBoxplot)
exportMethods(plotCCA)
exportMethods(plotColGraph)
exportMethods(plotColTile)
exportMethods(plotColTree)
exportMethods(plotDMNFit)
exportMethods(plotFeaturePrevalence)
exportMethods(plotForest)
exportMethods(plotHeatmap)
exportMethods(plotHistogram)
exportMethods(plotJointRPCA)
exportMethods(plotLoadings)
exportMethods(plotMediation)
exportMethods(plotOrdination)
exportMethods(plotPrevalence)
exportMethods(plotPrevalentAbundance)
exportMethods(plotRDA)
exportMethods(plotRowGraph)
exportMethods(plotRowPrevalence)
exportMethods(plotRowTile)
exportMethods(plotRowTree)
exportMethods(plotScree)
exportMethods(plotSeries)
exportMethods(plotTaxaPrevalence)
exportMethods(rowTreeData)
import(TreeSummarizedExperiment)
import(ggplot2)
import(ggraph)
import(methods)
import(mia)
importFrom(BiocGenerics,
  ncol,
  nrow
)
importFrom(BiocParallel,
  SerialParam,
  bpisup,
  bplapply,
  bpmapply,
  bpstart,
  bpstop
)
importFrom(DelayedArray,
  rowMeans,
  rowSums
)
importFrom(DirichletMultinomial,mixture)
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,
  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,
  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,
  scale_fill_viridis
)
