| f3a591a3 |
# Generated by roxygen2: do not edit by hand
|
| 080e467e |
export("Img<-")
|
| 93c8e11e |
export("ROIPoly<-")
|
| 947ad9f1 |
export("annotGeometries<-")
export("annotGeometry<-")
export("annotGeometryNames<-")
|
| e17f2c78 |
export("annotGraph<-")
export("annotGraphNames<-")
export("annotGraphs<-")
|
| 63b86054 |
export("cellSeg<-")
|
| 635b84ef |
export("centroids<-")
|
| c683b8d5 |
export("colData<-")
|
| 63b86054 |
export("colGeometries<-")
export("colGeometry<-")
export("colGeometryNames<-")
|
| e17f2c78 |
export("colGraph<-")
export("colGraphNames<-")
export("colGraphs<-")
|
| 63b86054 |
export("dimGeometries<-")
export("dimGeometry<-")
export("dimGeometryNames<-")
|
| 61c3c2e0 |
export("localResult<-")
export("localResultNames<-")
export("localResults<-")
|
| 63b86054 |
export("nucSeg<-")
export("rowGeometries<-")
export("rowGeometry<-")
export("rowGeometryNames<-")
|
| e17f2c78 |
export("rowGraph<-")
export("rowGraphNames<-")
export("rowGraphs<-")
|
| c683b8d5 |
export("spatialCoords<-")
|
| fd6c53a7 |
export("spatialGraph<-")
|
| e17f2c78 |
export("spatialGraphNames<-")
|
| fd6c53a7 |
export("spatialGraphs<-")
|
| 93c8e11e |
export("spotPoly<-")
|
| 63b86054 |
export("tissueBoundary<-")
export("txSpots<-")
|
| 08e2d3db |
export(.check_features)
|
| 7986a66a |
export(.check_rg)
|
| 08e2d3db |
export(.check_sample_id)
|
| 5049f898 |
export(.ext_)
|
| 08e2d3db |
export(.rm_empty_geometries)
export(.symbol2id)
export(.value2df)
export(.warn_symbol_duplicate)
|
| 8156d145 |
export(BioFormatsImage)
|
| 105c5f78 |
export(ExtImage)
|
| 93c8e11e |
export(ROIPoly)
|
| 14de0a39 |
export(SFEVersion)
|
| 578785a5 |
export(SpatRasterImage)
|
| f3a591a3 |
export(SpatialFeatureExperiment)
|
| 925b4f7a |
export(addSelectTx)
|
| 578785a5 |
export(addTxSpots)
|
| 925b4f7a |
export(addTxTech)
|
| 18281388 |
export(addVisiumSpotPoly)
|
| e04749f0 |
export(affine)
|
| ca3c5ca6 |
export(affineImg)
|
| 0670dc9e |
export(aggBboxes)
|
| 02812a8b |
export(aggregateTx)
export(aggregateTxTech)
|
| 947ad9f1 |
export(annotGeometries)
export(annotGeometry)
export(annotGeometryNames)
|
| e17f2c78 |
export(annotGraph)
export(annotGraphNames)
export(annotGraphs)
|
| 4e887f43 |
export(annotNPred)
|
| 2be67a29 |
export(annotOp)
export(annotPred)
|
| 1fde5d0d |
export(annotSummary)
|
| 6ce1cc84 |
export(bbox)
|
| 27881e5f |
export(bbox_center)
|
| 63b86054 |
export(cellSeg)
|
| 635b84ef |
export(centroids)
|
| e378387d |
export(changeSampleIDs)
|
| c683b8d5 |
export(colData)
|
| b13a520b |
export(colFeatureData)
|
| 63b86054 |
export(colGeometries)
export(colGeometry)
export(colGeometryNames)
|
| e17f2c78 |
export(colGraph)
export(colGraphNames)
export(colGraphs)
|
| ca989348 |
export(counts)
|
| 140c4707 |
export(crop)
|
| 8156d145 |
export(cropImg)
|
| 9c9475d9 |
export(df2sf)
|
| 63b86054 |
export(dimGeometries)
export(dimGeometry)
export(dimGeometryNames)
|
| aade74d9 |
export(findDebrisCells)
|
| 1869771b |
export(findSpatialNeighbors)
export(findVisiumGraph)
|
| ec25fb16 |
export(findVisiumHDGraph)
|
| 578785a5 |
export(formatTxSpots)
|
| 925b4f7a |
export(formatTxTech)
export(gdalParquetAvailable)
|
| b13a520b |
export(geometryFeatureData)
|
| f69540c3 |
export(getImg)
|
| b13a520b |
export(getParams)
|
| 0670dc9e |
export(getPixelSize)
|
| 7986a66a |
export(getTechTxFields)
|
| aade74d9 |
export(getTissueBoundaryConcave)
export(getTissueBoundaryImg)
|
| 0670dc9e |
export(imageIDs)
|
| f35481a9 |
export(imgData)
|
| 1e43b5e0 |
export(imgRaster)
|
| ca989348 |
export(imgSource)
|
| 1e43b5e0 |
export(isFull)
|
| 61c3c2e0 |
export(localResult)
|
| 7399d56d |
export(localResultAttrs)
export(localResultFeatures)
|
| 61c3c2e0 |
export(localResultNames)
export(localResults)
|
| ca989348 |
export(logcounts)
|
| f69540c3 |
export(mirror)
|
| ca989348 |
export(mirrorImg)
|
| 1870779b |
export(multi_listw2sparse)
|
| 63b86054 |
export(nucSeg)
|
| 27881e5f |
export(origin)
|
| 2b8d6ac9 |
export(read10xVisiumSFE)
|
| 845152bb |
export(readCosMX)
|
| 925b4f7a |
export(readSelectTx)
|
| ec25fb16 |
export(readVisiumHD)
|
| db728fc7 |
export(readVizgen)
|
| 3b2945c9 |
export(readXenium)
|
| ca989348 |
export(reducedDim)
|
| b13a520b |
export(reducedDimFeatureData)
|
| b8b00d8d |
export(removeEmptySpace)
|
| 1e43b5e0 |
export(rmvImg)
|
| 27881e5f |
export(rotate)
|
| ca989348 |
export(rotateImg)
|
| c683b8d5 |
export(rowData)
|
| b13a520b |
export(rowFeatureData)
|
| 63b86054 |
export(rowGeometries)
export(rowGeometry)
export(rowGeometryNames)
|
| e17f2c78 |
export(rowGraph)
export(rowGraphNames)
export(rowGraphs)
export(sampleIDs)
|
| e04749f0 |
export(scale)
|
| ca3c5ca6 |
export(scaleImg)
|
| c683b8d5 |
export(spatialCoords)
|
| f69540c3 |
export(spatialCoordsNames)
|
| fd6c53a7 |
export(spatialGraph)
|
| e17f2c78 |
export(spatialGraphNames)
|
| fd6c53a7 |
export(spatialGraphs)
|
| c876c74f |
export(splitByCol)
|
| 07eed593 |
export(splitComponent)
|
| 02812a8b |
export(splitContiguity)
export(splitSamples)
|
| 93c8e11e |
export(spotPoly)
|
| 140c4707 |
export(st_any_intersects)
export(st_any_pred)
|
| 4e887f43 |
export(st_n_intersects)
export(st_n_pred)
|
| 63b86054 |
export(tissueBoundary)
|
| 105c5f78 |
export(toExtImage)
|
| 1e43b5e0 |
export(toSpatRasterImage)
|
| fd6c53a7 |
export(toSpatialFeatureExperiment)
|
| ca3c5ca6 |
export(transformation)
|
| 27881e5f |
export(translate)
export(translateImg)
|
| f69540c3 |
export(transpose)
|
| db728fc7 |
export(transposeImg)
|
| 63b86054 |
export(txSpots)
|
| db728fc7 |
export(unit)
|
| 8156d145 |
exportClasses(BioFormatsImage)
|
| 105c5f78 |
exportClasses(ExtImage)
|
| db728fc7 |
exportClasses(SpatRasterImage)
|
| 9488968f |
exportClasses(SpatialFeatureExperiment)
|
| 080e467e |
exportMethods("Img<-")
|
| 8df945e0 |
exportMethods("[")
|
| 36dc14a2 |
exportMethods("annotGeometries<-")
exportMethods("annotGeometry<-")
exportMethods("annotGeometryNames<-")
|
| 63b86054 |
exportMethods("dimGeometries<-")
exportMethods("dimGeometry<-")
exportMethods("dimGeometryNames<-")
|
| 8156d145 |
exportMethods("ext<-")
|
| 61c3c2e0 |
exportMethods("localResult<-")
exportMethods("localResultNames<-")
exportMethods("localResults<-")
|
| fd6c53a7 |
exportMethods("spatialGraph<-")
|
| e17f2c78 |
exportMethods("spatialGraphNames<-")
|
| fd6c53a7 |
exportMethods("spatialGraphs<-")
|
| db728fc7 |
exportMethods(addImg)
|
| 9ec1fd8b |
exportMethods(affineImg)
|
| 02812a8b |
exportMethods(aggregate)
|
| 36dc14a2 |
exportMethods(annotGeometries)
exportMethods(annotGeometry)
exportMethods(annotGeometryNames)
|
| 6ce1cc84 |
exportMethods(bbox)
|
| 50abbe1a |
exportMethods(cbind)
|
| 77355441 |
exportMethods(containsOutOfMemoryData)
|
| 1e43b5e0 |
exportMethods(cropImg)
|
| 43ef1d5d |
exportMethods(dim)
|
| 63b86054 |
exportMethods(dimGeometries)
exportMethods(dimGeometry)
exportMethods(dimGeometryNames)
|
| 8156d145 |
exportMethods(ext)
|
| aade74d9 |
exportMethods(findDebrisCells)
|
| 1869771b |
exportMethods(findSpatialNeighbors)
|
| db728fc7 |
exportMethods(imgRaster)
exportMethods(imgSource)
|
| 27881e5f |
exportMethods(isFull)
|
| 61c3c2e0 |
exportMethods(localResult)
|
| 7399d56d |
exportMethods(localResultAttrs)
exportMethods(localResultFeatures)
|
| 61c3c2e0 |
exportMethods(localResultNames)
exportMethods(localResults)
|
| db728fc7 |
exportMethods(mirrorImg)
|
| 27881e5f |
exportMethods(origin)
|
| 8156d145 |
exportMethods(rotateImg)
|
| be42b5f8 |
exportMethods(saveRDS)
|
| ca3c5ca6 |
exportMethods(scaleImg)
|
| 887505e3 |
exportMethods(show)
|
| fd6c53a7 |
exportMethods(spatialGraph)
|
| e17f2c78 |
exportMethods(spatialGraphNames)
|
| fd6c53a7 |
exportMethods(spatialGraphs)
|
| be6ec631 |
exportMethods(splitByCol)
|
| 105c5f78 |
exportMethods(toExtImage)
|
| 1e43b5e0 |
exportMethods(toSpatRasterImage)
|
| afa9fa00 |
exportMethods(toSpatialFeatureExperiment)
|
| ca3c5ca6 |
exportMethods(transformation)
|
| 27881e5f |
exportMethods(translateImg)
|
| db728fc7 |
exportMethods(transposeImg)
exportMethods(unit)
|
| 14de0a39 |
exportMethods(updateObject)
|
| 8156d145 |
importClassesFrom(EBImage,Image)
|
| f3a591a3 |
importClassesFrom(SpatialExperiment,SpatialExperiment)
|
| db728fc7 |
importClassesFrom(SpatialExperiment,VirtualSpatialImage)
importClassesFrom(terra,SpatRaster)
|
| 50abbe1a |
importFrom(BiocGenerics,cbind)
|
| 77355441 |
importFrom(BiocGenerics,containsOutOfMemoryData)
importFrom(BiocGenerics,saveRDS)
|
| 14de0a39 |
importFrom(BiocGenerics,updateObject)
|
| a0b49147 |
importFrom(BiocNeighbors,AnnoyParam)
importFrom(BiocNeighbors,KmknnParam)
importFrom(BiocNeighbors,findKNN)
importFrom(BiocNeighbors,findNeighbors)
|
| 8d1d9667 |
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
|
| db728fc7 |
importFrom(BiocParallel,bpmapply)
|
| a296a7d0 |
importFrom(DropletUtils,read10xCounts)
|
| efed2e7c |
importFrom(EBImage,Image)
|
| aade74d9 |
importFrom(EBImage,closing)
importFrom(EBImage,fillHull)
importFrom(EBImage,makeBrush)
importFrom(EBImage,normalize)
importFrom(EBImage,otsu)
|
| a0b49147 |
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
|
| 4d13381e |
importFrom(S4Vectors,"mcols<-")
|
| b13a520b |
importFrom(S4Vectors,"metadata<-")
|
| 3105342e |
importFrom(S4Vectors,DataFrame)
|
| b6369a88 |
importFrom(S4Vectors,SimpleList)
|
| 47dd1de7 |
importFrom(S4Vectors,combineCols)
|
| 27881e5f |
importFrom(S4Vectors,isEmpty)
|
| afa9fa00 |
importFrom(S4Vectors,make_zero_col_DFrame)
|
| 4d13381e |
importFrom(S4Vectors,mcols)
|
| b13a520b |
importFrom(S4Vectors,metadata)
|
| 95b3456a |
importFrom(S4Vectors,setValidity2)
|
| 0670dc9e |
importFrom(S4Vectors,showAsCell)
|
| 07eed593 |
importFrom(S4Vectors,split)
|
| 1761ce70 |
importFrom(SingleCellExperiment,"altExp<-")
|
| ba2d9ecb |
importFrom(SingleCellExperiment,"int_colData<-")
importFrom(SingleCellExperiment,"int_elementMetadata<-")
importFrom(SingleCellExperiment,"int_metadata<-")
|
| 1761ce70 |
importFrom(SingleCellExperiment,"reducedDim<-")
|
| 47dd1de7 |
importFrom(SingleCellExperiment,"reducedDims<-")
|
| cbd53e06 |
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExp)
importFrom(SingleCellExperiment,altExpNames)
|
| d82f945e |
importFrom(SingleCellExperiment,counts)
|
| 63b86054 |
importFrom(SingleCellExperiment,int_colData)
importFrom(SingleCellExperiment,int_elementMetadata)
importFrom(SingleCellExperiment,int_metadata)
|
| ca989348 |
importFrom(SingleCellExperiment,logcounts)
|
| cbd53e06 |
importFrom(SingleCellExperiment,mainExpName)
|
| ca989348 |
importFrom(SingleCellExperiment,reducedDim)
|
| 47dd1de7 |
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,reducedDims)
|
| db728fc7 |
importFrom(SpatialExperiment,"imgData<-")
|
| b6369a88 |
importFrom(SpatialExperiment,"spatialCoords<-")
|
| d1612ca0 |
importFrom(SpatialExperiment,"spatialCoordsNames<-")
|
| f3a591a3 |
importFrom(SpatialExperiment,SpatialExperiment)
|
| db728fc7 |
importFrom(SpatialExperiment,addImg)
|
| f69540c3 |
importFrom(SpatialExperiment,getImg)
|
| db728fc7 |
importFrom(SpatialExperiment,imgData)
importFrom(SpatialExperiment,imgRaster)
importFrom(SpatialExperiment,imgSource)
importFrom(SpatialExperiment,mirrorImg)
|
| 1e43b5e0 |
importFrom(SpatialExperiment,rmvImg)
|
| 8156d145 |
importFrom(SpatialExperiment,rotateImg)
|
| afa9fa00 |
importFrom(SpatialExperiment,spatialCoords)
|
| 18281388 |
importFrom(SpatialExperiment,spatialCoordsNames)
|
| b1f6f929 |
importFrom(SpatialExperiment,toSpatialExperiment)
|
| 6cfb87df |
importFrom(SummarizedExperiment,"assay<-")
|
| ba2d9ecb |
importFrom(SummarizedExperiment,"colData<-")
|
| 50230d56 |
importFrom(SummarizedExperiment,"rowData<-")
|
| 02812a8b |
importFrom(SummarizedExperiment,assayNames)
|
| cbd53e06 |
importFrom(SummarizedExperiment,assays)
|
| ba2d9ecb |
importFrom(SummarizedExperiment,colData)
|
| 5887bca3 |
importFrom(SummarizedExperiment,rowData)
|
| d1612ca0 |
importFrom(data.table,":=")
|
| 02812a8b |
importFrom(data.table,as.data.table)
|
| c535ddcc |
importFrom(data.table,fread)
|
| 59341289 |
importFrom(data.table,is.data.table)
|
| b5822231 |
importFrom(data.table,merge.data.table)
|
| c535ddcc |
importFrom(data.table,rbindlist)
|
| f35481a9 |
importFrom(grDevices,col2rgb)
|
| 07c2ce3c |
importFrom(lifecycle,deprecate_warn)
importFrom(lifecycle,deprecated)
importFrom(lifecycle,is_present)
|
| 1761ce70 |
importFrom(methods,"slot<-")
|
| 8985a653 |
importFrom(methods,as)
|
| 887505e3 |
importFrom(methods,callNextMethod)
|
| b0947971 |
importFrom(methods,is)
|
| 63b86054 |
importFrom(methods,new)
|
| afa9fa00 |
importFrom(methods,setAs)
|
| f3a591a3 |
importFrom(methods,setClass)
|
| be42b5f8 |
importFrom(methods,setClassUnion)
|
| afa9fa00 |
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setReplaceMethod)
|
| 8985a653 |
importFrom(methods,show)
|
| 080e467e |
importFrom(methods,signature)
|
| cbd53e06 |
importFrom(methods,slot)
|
| 3f95c646 |
importFrom(methods,slotNames)
|
| 8985a653 |
importFrom(methods,validObject)
|
| 2b8d6ac9 |
importFrom(rjson,fromJSON)
|
| aade74d9 |
importFrom(rlang,"!!")
|
| 619a6cae |
importFrom(rlang,"%||%")
|
| aade74d9 |
importFrom(rlang,.data)
|
| f69540c3 |
importFrom(rlang,check_installed)
|
| aade74d9 |
importFrom(rlang,sym)
|
| b5c3ff26 |
importFrom(sf,"st_agr<-")
|
| f35481a9 |
importFrom(sf,"st_geometry<-")
|
| 0682864f |
importFrom(sf,st_agr)
|
| db728fc7 |
importFrom(sf,st_area)
|
| 59341289 |
importFrom(sf,st_as_sf)
|
| b5c3ff26 |
importFrom(sf,st_as_sfc)
|
| 6ce1cc84 |
importFrom(sf,st_bbox)
|
| f3a591a3 |
importFrom(sf,st_buffer)
|
| 050ef713 |
importFrom(sf,st_cast)
|
| 63b86054 |
importFrom(sf,st_centroid)
|
| 02812a8b |
importFrom(sf,st_collection_extract)
|
| 63b86054 |
importFrom(sf,st_coordinates)
|
| 33fd1f76 |
importFrom(sf,st_covers)
|
| 4e887f43 |
importFrom(sf,st_disjoint)
|
| db728fc7 |
importFrom(sf,st_distance)
|
| b5c3ff26 |
importFrom(sf,st_drop_geometry)
|
| 3105342e |
importFrom(sf,st_geometry)
|
| 887505e3 |
importFrom(sf,st_geometry_type)
|
| f3a591a3 |
importFrom(sf,st_geometrycollection)
|
| 0682864f |
importFrom(sf,st_intersection)
|
| 140c4707 |
importFrom(sf,st_intersects)
|
| 4e887f43 |
importFrom(sf,st_is_empty)
|
| b0947971 |
importFrom(sf,st_is_valid)
|
| 3ddb57b0 |
importFrom(sf,st_join)
|
| f3a591a3 |
importFrom(sf,st_linestring)
|
| 02812a8b |
importFrom(sf,st_make_grid)
|
| f3a591a3 |
importFrom(sf,st_multilinestring)
importFrom(sf,st_multipoint)
importFrom(sf,st_multipolygon)
|
| db728fc7 |
importFrom(sf,st_nearest_feature)
|
| f3a591a3 |
importFrom(sf,st_point)
importFrom(sf,st_polygon)
|
| b13a520b |
importFrom(sf,st_read)
|
| f3a591a3 |
importFrom(sf,st_sf)
importFrom(sf,st_sfc)
|
| aade74d9 |
importFrom(sf,st_simplify)
|
| 0682864f |
importFrom(sf,st_union)
|
| 8156d145 |
importFrom(sf,st_z_range)
importFrom(sf,st_zm)
importFrom(sfheaders,sf_linestring)
importFrom(sfheaders,sf_multilinestring)
importFrom(sfheaders,sf_multipoint)
importFrom(sfheaders,sf_multipolygon)
importFrom(sfheaders,sf_polygon)
|
| 5f716260 |
importFrom(spatialreg,as_dgRMatrix_listw)
|
| a0b49147 |
importFrom(spdep,card)
|
| 1869771b |
importFrom(spdep,dnearneigh)
importFrom(spdep,gabrielneigh)
importFrom(spdep,graph2nb)
importFrom(spdep,knearneigh)
importFrom(spdep,knn2nb)
|
| 5f716260 |
importFrom(spdep,mat2listw)
|
| 07eed593 |
importFrom(spdep,n.comp.nb)
|
| 1869771b |
importFrom(spdep,nb2listw)
|
| 9d7eb8cd |
importFrom(spdep,nb2listwdist)
|
| 1869771b |
importFrom(spdep,poly2nb)
importFrom(spdep,relativeneigh)
importFrom(spdep,soi.graph)
importFrom(spdep,tri2nb)
|
| b5c3ff26 |
importFrom(stats,aggregate)
|
| bf421dae |
importFrom(stats,median)
|
| 6b676150 |
importFrom(stats,na.omit)
|
| a7d6df20 |
importFrom(stats,setNames)
|
| db728fc7 |
importFrom(terra,"ext<-")
|
| 9146938f |
importFrom(terra,as.raster)
|
| db728fc7 |
importFrom(terra,ext)
|
| e04749f0 |
importFrom(terra,inMemory)
|
| 578785a5 |
importFrom(terra,nlyr)
|
| db728fc7 |
importFrom(terra,rast)
|
| 27881e5f |
importFrom(terra,shift)
|
| 07c2ce3c |
importFrom(terra,sources)
|
| be42b5f8 |
importFrom(terra,unwrap)
|
| db728fc7 |
importFrom(terra,vect)
|
| be42b5f8 |
importFrom(terra,wrap)
|
| 578785a5 |
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
|
| 95b3456a |
importFrom(utils,getFromNamespace)
|
| e050de2b |
importFrom(utils,head)
|
| 14de0a39 |
importFrom(utils,packageVersion)
|
| b1f6f929 |
importFrom(utils,read.csv)
|
| d1612ca0 |
importFrom(utils,tail)
|
| 925b4f7a |
importFrom(zeallot,"%<-%")
|
