Package index • XenSCE

All functions
`XenSCE-class`	define container for Xenium demo data
`XenSPEP-class`	manage SpatialExperiment with parquet references
`XenSPEP()`	XenSPEP (SpatialExperiment with parquet references) constructor
`build_demo()`	build a XenSCE instance for GBM demo data from TENx
`build_panc_subset()`	build a XenSCE instance based on the SFEData XeniumOutput element
`cache_assets()`	return paths to cached entities after retrieving and caching them if needed
`cache_demo()`	helper for caching a built demo XenSCE
`cache_mtif()`	cache and/or retrieve path to an ome.tif file for demonstration
`cache_panc_subset()`	cache and/or retrieve path to zipped pancreas subset (originally from SFEData)
`cache_sfeLung()`	cache and/or retrieve path to an SFE of V1 lung demo data from 10x
`cache_sfeLung_ntx()`	cache and/or retrieve path to an SFE of V1 lung demo data from 10x
`cache_xen_luad()`	cache and/or retrieve path to Xenium Lung Adenocarcinoma example data, zipped SPEP accompanied by parquet
`cache_xen_prost()`	cache and/or retrieve path to xenium human prostate adenocarcinoma, 5k genes
`cache_xen_sk()`	cache and/or retrieve path to xenium human primary melanoma, 5k genes
`clip_rect()`	restrict XenSCE to cells with centroids in specified rectangle, also restrict boundary and transcript location features
`demoapp()`	simple app to explore an image
`e2sym()`	helper function to map ENS ids to symbols
`e79sym`	mapping from ENSG to symbols based on EnsDb.Hsapiens.v79
`getCellBoundaries(<XenSCE>)`	method for cell boundary extraction
`getCellBoundaries(<XenSPEP>)`	method for cell boundary extraction
`getCellBoundaries()`	method for cell boundary extraction
`getNucleusBoundaries(<XenSCE>)`	method for nucleus boundary extraction
`getNucleusBoundaries(<XenSPEP>)`	method for nucleus boundary extraction
`getNucleusBoundaries()`	method for nucleus boundary extraction
`getTranscripts(<XenSCE>)`	method for transcript extraction
`getTranscripts(<XenSPEP>)`	method for transcript extraction
`getTranscripts()`	method for transcript extraction
`ggprep_seg()`	prepare a XenSPEP for ggplot2 visualization
`ingest_xen()`	produce a pre-loaded XenSPEP (SpatialExperiment with parquet references)
`loadGeometry(<XenSPEP>)`	read and bind parquet data to XenSPEP
`loadGeometry()`	read and bind parquet data to XenSPEP
`panc_sub`	example XenSCE instance based on pancreas subset from SFEData XeniumOutput
`plotCellBoundaries()`	render boundaries of cells with optional centroid positions and transcript positions
`plot_xen_ggprep()`	plot method for ggplot2-prepared XenSPEP
`print_xen_ggprep()`	print method for ggplot2-prepared XenSPEP
`reset_parq_paths()`	utility for dealing with cached Xen_SPEP in temp folder
`restoreZipXenSPEP()`	use unzip, readRDS, and loadGeometry to restore a XenSPEP
`retrieve_demo()`	retrieve cached demo XenSCE
`sfe2xsce()`	convert SpatialFeatureExperiment to XenSCE
`show(<XenSCE>)`	summarize XenSCE
`show(<XenSPEP>)`	display aspects of XenSPEP
`[`(<XenSPEP>,<ANY>,<ANY>,<ANY>)	formal bracket definition, that leaves parquet geometry information alone.
`view_seg()`	naive polygon viewer
`view_seg_g2()`	naive polygon viewer, will indicate presence of transcripts for two genes in cells
`xdims()`	helper function for XenSCE show method, producing dimensions for geometry information
`zipXenSPEP()`	serialize the collection of XenSPEP and parquet with zip

Reference

All functions