spatIDs-generic: Spatial and feature IDs

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Spatial and feature IDs

Description

Get the cell IDs (termed spatial IDs to better reflect when not at the single-cell level) and feature IDs of a giotto object or subobject

Usage

spatIDs(x, spat_unit, ...)

featIDs(x, feat_type, ...)

## Default S4 method for signatures:
## 'giotto', 'exprObj', 'spatLocsObj', 'cellMetaObj', 'spatialNetworkObj' 'dimObj'

## S4 method for signature 'giotto,missing'
spatIDs(x, spat_unit, ...)

## S4 method for signature 'giotto,character'
spatIDs(x, spat_unit, ...)

## S4 method for signature 'exprObj,missing'
spatIDs(x, spat_unit, ...)

## S4 method for signature 'spatLocsObj,missing'
spatIDs(x, spat_unit, ...)

## S4 method for signature 'cellMetaObj,missing'
spatIDs(x, spat_unit, ...)

## S4 method for signature 'spatialNetworkObj,missing'
spatIDs(x, spat_unit, ...)

## S4 method for signature 'dimObj,missing'
spatIDs(x, spat_unit, ...)

## S4 method for signature 'giottoPolygon,missing'
spatIDs(x, use_cache = TRUE, ...)

## S4 method for signature 'spatEnrObj,missing'
spatIDs(x, spat_unit, ...)

## S4 method for signature 'nnNetObj,missing'
spatIDs(x, spat_unit, ...)

## S4 method for signature 'giotto,missing'
featIDs(x, feat_type, ...)

## S4 method for signature 'giotto,character'
featIDs(x, feat_type, ...)

## S4 method for signature 'exprObj,missing'
featIDs(x, feat_type, ...)

## S4 method for signature 'giottoPoints,missing'
featIDs(x, use_cache = TRUE, ...)

## S4 method for signature 'spatEnrObj,missing'
featIDs(x, feat_type, ...)

Arguments

x	an object
spat_unit	(optional) specify which spatial unit
...	additional parameters to pass
use_cache	use cached IDs if available (gpoly and gpoints only)
feat_type	(optional) specify which feature type

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.