Create S4 spatEnrObj
Usage
createSpatEnrObj(
enrichment_data,
name = "test",
spat_unit = "cell",
feat_type = "rna",
method = NULL,
provenance = NULL,
misc = NULL,
verbose = TRUE
)Arguments
- enrichment_data
spatial enrichment results, provided a dataframe-like object
- name
name of S4 spatEnrObj
- spat_unit
spatial unit of aggregated expression (e.g. 'cell')
- feat_type
feature type of aggregated expression (e.g. 'rna', 'protein')
- method
method used to generate spatial enrichment information
- provenance
origin data of aggregated expression information (if applicable)
- misc
misc additional information about the spatial enrichment or how it was generated
- verbose
be verbose
Examples
x <- GiottoData::loadSubObjectMini("spatEnrObj")
createSpatEnrObj(
enrichment_data = slot(x, "enrichDT"),
name = "cluster_metagene"
)
#> There are non numeric or integer columns for the spatial
#> enrichment input at column position(s): 6
#> The first non-numeric column will be considered as a cell ID to test for
#> consistency with the expression matrix.
#> Other non-numeric columns will be removed.
#> An object of class spatEnrObj : "cluster_metagene"
#> spat_unit : "cell"
#> feat_type : "rna"
#> ------------------------
#>
#> preview:
#> 1 2 3 4 5
#> <num> <num> <num> <num> <num>
#> 1: 1.014837 0.0000000 0.3160792 0.0000000 0
#> 2: 3.207415 0.9579716 0.6728505 0.2132677 0
#> 3: 3.953661 0.4604975 0.0000000 0.2302488 0
#> cell_ID
#> <char>
#> 1: 240649020551054330404932383065726870513
#> 2: 274176126496863898679934791272921588227
#> 3: 323754550002953984063006506310071917306
#>
#> ...first 20 remaining colnames:
#>
#>
#>
#>