# Generated by roxygen2: do not edit by hand

S3method("$",VoltRon)
S3method("$<-",VoltRon)
S3method(.DollarNames,VoltRon)
S3method(as.VoltRon,Seurat)
S3method(as.VoltRon,SpatialExperiment)
S3method(as.Zarr,"magick-image")
export("vrCoordinates<-")
export("vrEmbeddings<-")
export("vrFeatureData<-")
export("vrGraph<-")
export("vrImages<-")
export("vrMainAssay<-")
export("vrMainChannel<-")
export("vrMainFeatureType<-")
export("vrMainImage<-")
export("vrMainSpatial<-")
export("vrSegments<-")
export("vrSpatialPoints<-")
export(FromSegmentToCrop)
export(Metadata)
export(SampleMetadata)
export(addAssay)
export(addBlockConnectivity)
export(addFeature)
export(addMetadata)
export(addSpatialLayer)
export(annotateSpatialData)
export(as.AnnData)
export(as.Giotto)
export(as.OmeTiff)
export(as.OmeZarr)
export(as.Seurat)
export(as.SpatialExperiment)
export(as.VoltRon)
export(as.Zarr)
export(combineChannels)
export(combineGraphs)
export(convertAnnDataToVoltRon)
export(fixVoltRon)
export(flipCoordinates)
export(formAssay)
export(formSpatial)
export(formVoltRon)
export(generateCosMxImage)
export(generateGeoJSON)
export(generateSegments)
export(generateTileData)
export(generateXeniumImage)
export(getBasilisk)
export(getClusters)
export(getDeconvolution)
export(getDiffExp)
export(getFeatures)
export(getHotSpotAnalysis)
export(getNicheAssay)
export(getOmeTiffChannels)
export(getPCA)
export(getProfileNeighbors)
export(getRcppAutomatedRegistration)
export(getRcppManualRegistration)
export(getSpatialNeighbors)
export(getUMAP)
export(getVariableFeatures)
export(import10Xh5)
export(importCosMx)
export(importDBITSeq)
export(importGenePS)
export(importGeoMx)
export(importImageData)
export(importOpenST)
export(importPhenoCycler)
export(importQuPathIF)
export(importSTOmics)
export(importVisium)
export(importVisiumHD)
export(importXenium)
export(loadVoltRon)
export(modulateImage)
export(normalizeData)
export(open_zarr)
export(registerSpatialData)
export(resizeImage)
export(saveVoltRon)
export(transferData)
export(updateAssay)
export(vrAssayNames)
export(vrAssayParams)
export(vrAssayTypes)
export(vrBarPlot)
export(vrCoordinates)
export(vrData)
export(vrEmbeddingFeaturePlot)
export(vrEmbeddingNames)
export(vrEmbeddingPlot)
export(vrEmbeddings)
export(vrFeatureData)
export(vrFeatureTypeNames)
export(vrFeatures)
export(vrGraph)
export(vrGraphNames)
export(vrHeatmapPlot)
export(vrImageChannelNames)
export(vrImageNames)
export(vrImages)
export(vrMainAssay)
export(vrMainChannel)
export(vrMainFeatureType)
export(vrMainImage)
export(vrMainSpatial)
export(vrNeighbourhoodEnrichment)
export(vrNeighbourhoodEnrichmentPlot)
export(vrProportionPlot)
export(vrSampleNames)
export(vrScatterPlot)
export(vrSegments)
export(vrSpatialFeaturePlot)
export(vrSpatialNames)
export(vrSpatialPlot)
export(vrSpatialPoints)
export(vrViolinPlot)
export(warpImage)
export(warpSimpleITKImage)
export(zarrcreateGroup)
exportClasses(VoltRon)
exportClasses(vrAssay)
exportClasses(vrAssayV2)
exportClasses(vrBlock)
exportClasses(vrImage)
exportClasses(vrLayer)
exportClasses(vrMetadata)
exportClasses(vrSample)
exportClasses(vrSpatial)
exportMethods("Metadata<-")
exportMethods("[[")
exportMethods("[[<-")
exportMethods("vrCoordinates<-")
exportMethods("vrEmbeddings<-")
exportMethods("vrFeatureData<-")
exportMethods("vrImages<-")
exportMethods("vrMainAssay<-")
exportMethods("vrMainChannel<-")
exportMethods("vrMainFeatureType<-")
exportMethods("vrMainImage<-")
exportMethods("vrMainSpatial<-")
exportMethods("vrSegments<-")
exportMethods("vrSpatialPoints<-")
exportMethods(Metadata)
exportMethods(addAssay)
exportMethods(addFeature)
exportMethods(combineChannels)
exportMethods(flipCoordinates)
exportMethods(generateTileData)
exportMethods(getFeatures)
exportMethods(getPCA)
exportMethods(merge)
exportMethods(modulateImage)
exportMethods(normalizeData)
exportMethods(resizeImage)
exportMethods(subset)
exportMethods(transferData)
exportMethods(updateAssay)
exportMethods(vrAssayNames)
exportMethods(vrAssayTypes)
exportMethods(vrCoordinates)
exportMethods(vrData)
exportMethods(vrEmbeddingNames)
exportMethods(vrEmbeddings)
exportMethods(vrFeatureData)
exportMethods(vrFeatureTypeNames)
exportMethods(vrFeatures)
exportMethods(vrImageChannelNames)
exportMethods(vrImageNames)
exportMethods(vrImages)
exportMethods(vrMainAssay)
exportMethods(vrMainChannel)
exportMethods(vrMainFeatureType)
exportMethods(vrMainImage)
exportMethods(vrMainSpatial)
exportMethods(vrSampleNames)
exportMethods(vrSegments)
exportMethods(vrSpatialNames)
exportMethods(vrSpatialPoints)
import(ggplot2)
import(shiny)
importClassesFrom(Matrix,Matrix)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(Matrix,dgRMatrix)
importClassesFrom(Matrix,dgeMatrix)
importClassesFrom(S4Arrays,Array)
importClassesFrom(data.table,data.table)
importFrom(BiocSingular,
  FastAutoParam,
  runPCA
)
importFrom(EBImage,
  as.Image,
  colorMode,
  imageData,
  writeImage
)
importFrom(Matrix,
  Matrix,
  colSums,
  rowMeans,
  rowSums,
  sparseMatrix,
  t
)
importFrom(RANN,nn2)
importFrom(RCDT,delaunay)
importFrom(RcppAnnoy,
  AnnoyEuclidean,
  AnnoyManhattan
)
importFrom(S4Vectors,DataFrame)
importFrom(data.table,
  alloc.col,
  as.data.table,
  chmatch,
  data.table,
  fread,
  is.data.table,
  melt,
  set,
  setkey
)
importFrom(dplyr,
  "%>%",
  add_row,
  arrange,
  as_tibble,
  bind_cols,
  bind_rows,
  coalesce,
  desc,
  distinct,
  filter,
  full_join,
  group_by,
  left_join,
  mutate,
  mutate_all,
  n,
  n_distinct,
  right_join,
  select,
  summarize,
  tibble
)
importFrom(ggplot2,
  annotation_custom,
  annotation_raster,
  coord_fixed,
  geom_rect,
  ggplot,
  ggproto,
  xlim,
  ylim
)
importFrom(ggpubr,ggarrange)
importFrom(ggrepel,geom_label_repel)
importFrom(grDevices,
  as.raster,
  col2rgb,
  hcl,
  rgb,
  rgb2hsv
)
importFrom(grid,
  gpar,
  pointsGrob,
  rasterGrob,
  unit
)
importFrom(ids,random_id)
importFrom(igraph,
  "E<-",
  "V<-",
  E,
  V,
  add_edges,
  as_adjacency_matrix,
  as_data_frame,
  cluster_leiden,
  components,
  disjoint_union,
  edge_attr_names,
  get.data.frame,
  graph_from_adjacency_matrix,
  graph_from_edgelist,
  induced_subgraph,
  make_empty_graph,
  neighborhood,
  set_edge_attr,
  simplify,
  subgraph,
  union,
  vcount,
  vertices
)
importFrom(magick,
  as_EBImage,
  geometry_size_percent,
  image_blank,
  image_composite,
  image_contrast,
  image_convert,
  image_crop,
  image_data,
  image_flip,
  image_flop,
  image_ggplot,
  image_info,
  image_join,
  image_modulate,
  image_negate,
  image_raster,
  image_read,
  image_resize,
  image_rotate,
  image_scale,
  image_write
)
importFrom(methods,
  "slot<-",
  as,
  is,
  new,
  slot,
  slotNames
)
importFrom(rjson,fromJSON)
importFrom(rlang,
  "%||%",
  '!!',
  dots_list,
  enquo,
  eval_tidy,
  list2,
  quo_get_expr,
  quo_name,
  quo_text,
  sym
)
importFrom(shiny,
  HTML,
  reactiveValuesToList,
  tags,
  validateCssUnit
)
importFrom(shinyjs,
  hide,
  show,
  useShinyjs
)
importFrom(sp,point.in.polygon)
importFrom(stats,
  aggregate,
  as.formula,
  cutree,
  dist,
  hclust,
  kmeans,
  loess,
  median,
  na.omit,
  pnorm,
  predict,
  quantile,
  setNames,
  var
)
importFrom(stringr,
  str_extract,
  str_order,
  str_pad,
  str_remove,
  str_replace,
  str_sort
)
importFrom(utils,
  .DollarNames,
  capture.output,
  head,
  read.csv,
  read.table,
  write.table
)
importFrom(uwot,umap)
useDynLib(VoltRon)
