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Divide SPE object into smaller objects by column features

split_spe.Rd

split_spe() splits an SPE object into smaller objects by a column feature. Ideally this should be in the SpatialExperiment class or some utility package.

Usage

split_spe(spe, split_colname, assay_name = NULL)

Arguments

spe

SpatialExperiment object containing spatial omics data and spatial diffex results

split_colname

Column of rowData that maps to gene set

assay_name

Optional name of assay to use in split data

Value

A list of SpatialExperiment objects containing a subset of the data

Examples

data(smallPancData)
data(pancMeta)
data(protMeta)
pooledPanc <- dplyr::bind_cols(smallPancData)
panc.spe <- convert_to_spe(pooledPanc, pancMeta, protMeta, 
          feature_meta_colname = "pancProts")
#> Spatial object created without spatial coordinate 
#>          column names provided. Distance based analysis will not be enabled.
#> Note: Only mapping metadata for 2986 features out of 3000 data points
split_list <- split_spe(panc.spe, split_colname = "Image")
#> Spatial object created without spatial coordinate 
#>          column names provided. Distance based analysis will not be enabled.
#> Spatial object created without spatial coordinate 
#>          column names provided. Distance based analysis will not be enabled.
#> Spatial object created without spatial coordinate 
#>          column names provided. Distance based analysis will not be enabled.