Import a Stereo-seq assay

Giotto import functionalities for Stereo-seq datasets. This function generates a `StereoSeqReader` instance with convenient reader functions for loading individual pieces of Stereo-seq data into Giotto-compatible representations when the param `stereoseq_dir` is provided. A function that creates the full `giotto` object is also available. These functions should have all param values provided as defaults, but can be flexibly modified to look in alternative directories or paths.

importStereoSeq(
  stereoseq_dir = NULL,
  type = c("bin", "cell"),
  bin_size = "bin100",
  gene_column = c("geneName", "geneID"),
  negative_y = TRUE,
  gef_type = NULL
)

# S4 method for class 'StereoSeqReader,missing'
plot(x, y, ...)

Arguments

stereoseq_dir

filepath to the Stereo-seq `outs` directory.

type

character. One of `"bin"` (square bin, default) or `"cell"` (cell bin / cellbin).

bin_size

character. Bin size level to load when `type = "bin"`. One of `"bin1"`, `"bin5"`, `"bin10"`, `"bin20"`, `"bin50"`, `"bin100"`, `"bin150"`, `"bin200"`. Default is `"bin100"`. List available bins in your sample with `rhdf5::h5ls("path/to/*.tissue.gef")`.

gene_column

character. Which column to use as feature identifiers. One of `"geneName"` (default) or `"geneID"`.

negative_y

logical. Map data to negative y spatial values (default `TRUE`). Origin is placed at the upper-left instead of lower-left.

x

`StereoSeqReader`

...

additional params to pass

Value

`StereoSeqReader` object

Details

Loading functions are generated after `stereoseq_dir` is set.

Examples

if (FALSE) { # \dontrun{
# Create a StereoSeqReader
reader <- importStereoSeq(
    stereoseq_dir = "path/to/outs",
    type = "bin",
    bin_size = "bin100"
)

# Load expression or spatial locations individually
expr   <- reader$load_expression()
sl     <- reader$load_spatlocs()
img    <- reader$load_image()

# Create a full giotto object
g <- reader$create_gobject()

# Change bin size and recreate
reader$bin_size <- "bin50"
g <- reader$create_gobject()
} # }