Package index • Kandinsky

All functions
`AddTxPath()`	Add transcript file path to Kandinsky data in a Seurat object
`AlignXeniumCoords()`	align Xenium image and cell coordinates
`CosmxFovPlot()`	Visualize CosMx IFs staining for a list of FOVs
`EnrichPlots()`	Combined PropPlot and ResidualPlot
`GetTxData()`	Query and filter Kandinsky transcript file
`KanData<-`()	Assign data to Kandinsky
`KanData()` `KanData<-`(<Kandinsky>) `KanData<-`(<Seurat>)	Show Kandinsky data
`KanPlot()`	visualize Kandinsky and Seurat spatial data
`Kandinsky-class` `Kandinsky`	Kandinsky S4 object class
`LoadXeniumImage()`	Load Xenium OME tiff image
`PackedSpatRaster()`	S4 Class Union KanImg
`PropPlot()`	Proportion barplot
`ResidualPlot()`	Chi-square test residual plot
`SlidePlot()`	Plot Kandinsky images
`addKanData()`	Add Kandinsky data from .rds file to Seurat object
`c12`	C12 discrete color palette
`c24`	C24 discrete color palette
`centroid_nb()`	centroid distance neighbour identification
`fireflyPlot()`	Plot minimum distance between cell types as a spatial heatmap
`get_nbcounts()`	Get neighbourhood aggregated gene expression count matrix
`get_visium_textures()`	Extract texture features from Visium image
`global_biv_spatcor()`	Compute global bivariate spatial correlation
`global_univ_spatcor()`	Compute global Moran's I spatial autocorrelation statistic
`he_mask()`	Mask Visium H&E image
`hotspot_analysis()`	Hotspot analysis using Getis-Ord Gi* statistics
`hotspot_count()`	Count and describe Getis-Ord Gi* hotspot sites
`hotspot_overlap()`	define overlap between hot/cold spots of two variables
`jc_coloc()`	JC colocalization test and plot using Seurat/Kandinsky object
`kandinsky_init()`	Initialize Kandinsky data
`knn_nb()`	K-nearest neighbour neighbour identification
`load_g4x_img()`	Create spatraster image from G4X jp2 image file
`membrane_nb()`	membrane-based neighbour identification
`multi_jc()`	same-color (BB) and different-color (BW) join count test
`nbCluster()`	Identify single cell/spot clusters on the basis of their neighbourhood compositin
`nbSizePlot()`	density plot of neighbourhood size across cells/spots
`nb_expand()`	expand neighbour links to N higher orders
`nb_summary()`	Get Kandinsky neighbourhood summary metrics
`nb_update()`	Update definition of Kandinsky neighbour network
`nnMat()`	Neighbour composition matrix
`nn_query()`	Interrogate neighbour matrix
`populate_sf()`	Add variables to sf object stored in Kandinsky data
`prepare_cosmx_seurat()`	Prepare NanoString Cosmx Seurat data
`prepare_g4x_seurat()`	Prepare Singular Genomics G4X Seurat data
`prepare_merscope_seurat()`	Prepare Vizgen Merscope Seurat data
`prepare_proseg_seurat()`	Prepare proseg Seurat data
`prepare_seurat_other()`	prepare seurat object starting from any spatial transcriptomic/proteomic data in tabular format
`prepare_slideseq_seurat()`	Prepare Slide-Seq Seurat data
`prepare_visiumHD_seurat()`	Prepare 10X Visium HD Seurat data
`prepare_visium_seurat()`	Prepare 10X Visium Seurat data
`prepare_xenium_seurat()`	Prepare 10X Xenium Seurat data
`queen_nb()`	queen contiguity neighbour identification
`readKanData()`	Read Kandinsky data
`read_fovfile()`	Read CosMx fov position file
`resample_cells()`	resample single cells in Seurat object
`saveKanData()`	Save Kandinsky data
`scale_coords()`	Rescale Kandinsky polygon xy coordinates
`smi2sf()`	Create sf geometry object from CosMx Seurat data
`spweights_mat()`	estimate weight summary constansts from spatial weights matrix
`stitch_samples()`	Merge coordinate reference systems from independent samples
`tri_nb()`	Delaunay triangulation neighbour identification
`update_kandinsky()`	Update Kandinsky data
`visium2rast()`	Create spatraster image from Visium image file
`visium2sf()`	Create sf geometry object from Visium Seurat data

Reference

All functions