Binarize values to 0 and 1 based on a minimal value. For matrices, the default threshold is 0. For rasters, the default is a value determined through sampled (5e5 pixels) otsu.
Value
binarizeThreshParam
params
threshold | numeric (optional) Values above or equal to the threshold will be set to 1. Below will be set to 0. If not provided, defaults to 0 for matrices and a value determined by otsu for rasters. |
drop0 | logical (only for dgCMatrix, default = FALSE) Whether to
run Matrix::drop0 after binarization |
See also
Other threshold parameters:
threshold_minmax
Examples
e <- GiottoData::loadSubObjectMini("exprObj")
# also works with matrix classes
bin_e <- processData(e, thresholdParam("binarize"))
force(bin_e)
#> An object of class exprObj : "custom"
#> spat_unit : "aggregate"
#> feat_type : "rna"
#> provenance: z0 z1
#>
#> contains:
#> 337 x 462 sparse Matrix of class "dgCMatrix"
#>
#> Mlc1 . . . . . . 1 . . 1 . . . ......
#> Gprc5b . 1 . 1 . . 1 . 1 1 . 1 . ......
#> Gfap 1 . 1 1 . . 1 . 1 1 . . . ......
#>
#> ........suppressing 449 columns and 331 rows
#>
#> Adgrf4 . . . . . . . . . . . . . ......
#> Epha2 . . . . . . . . . . . . . ......
#> Blank-139 . . . . . . . . . . . . . ......
#>
#> First four colnames:
#> 240649020551054330404932383065726870513
#> 274176126496863898679934791272921588227
#> 323754550002953984063006506310071917306
#> 87260224659312905497866017323180367450
gimg <- GiottoData::loadSubObjectMini("giottoLargeImage")
# also works with SpatRasters
bin_img <- processData(gimg, thresholdParam("binarize"))
plot(bin_img)
