Create Stereo-seq Giotto Object
createGiottoStereoSeqObject(
stereoseq_dir,
type = "squarebin",
bin_size = "bin100",
gene_column = "geneName",
negative_y = TRUE,
shift_polygon_y = 0,
verbose = TRUE,
h5_file = NULL,
instructions = NULL
)filepath to the exported Stereo-seq directory.
character. Use "squarebin" to read expression at different bin levels (default), "cellbin" to read expression at cell resolution, or "subcellular" to read individual transcripts and cell boundaries.
bin size. Choose a value from "bin1", "bin5", "bin10", "bin20", "bin50", "bin100", "bin150", or "bin200". List the available bins in your sample using rhdf5::h5ls("path/to/*.tissue.gef"). Only needed when using type = "squarebin".
(optional) character. Which column contains the gene names within the geneExp information. Choose from "geneName" (default), or "geneID"
logical. Map data to negative y spatial values during
automatic alignment (Default = TRUE). Meaning that origin is in upper left
instead of lower left.
from createGiottoInstructions
logical. Be verbose.
(optional) name to create an on-disk HDF5 file.
list of instructions or output result
Giotto Stereo-seq object
This function is deprecated. Use [createGiottoStereoSeqObjectBin()] for square bin data or [createGiottoStereoSeqObjectCell()] for cell bin data. The `"subcellular"` type is still only available through this function.
[importStereoSeq()] [createGiottoStereoSeqObjectBin()] [createGiottoStereoSeqObjectCell()]