LoadXenium {Seurat} | R Documentation |
Read and Load 10x Genomics Xenium in-situ data
Description
Read and Load 10x Genomics Xenium in-situ data
Usage
LoadXenium(
data.dir,
fov = "fov",
assay = "Xenium",
mols.qv.threshold = 20,
cell.centroids = TRUE,
molecule.coordinates = TRUE,
segmentations = NULL,
flip.xy = FALSE
)
ReadXenium(
data.dir,
outs = c("segmentation_method", "matrix", "microns"),
type = "centroids",
mols.qv.threshold = 20,
flip.xy = F
)
Arguments
data.dir |
Directory containing all Xenium output files with default filenames |
fov |
FOV name |
assay |
Assay name |
mols.qv.threshold |
Remove transcript molecules with a QV less than this threshold. QV >= 20 is the standard threshold used to construct the cell x gene count matrix. |
cell.centroids |
Whether or not to load cell centroids |
molecule.coordinates |
Whether or not to load molecule pixel coordinates |
segmentations |
One of "cell", "nucleus" or NULL (to load either cell segmentations, nucleus segmentations or neither) |
flip.xy |
Whether or not to flip the x/y coordinates of the Xenium outputs to match what is displayed in Xenium Explorer, or fit on your screen better. |
outs |
Types of molecular outputs to read; choose one or more of:
|
type |
Type of cell spatial coordinate matrices to read; choose one or more of:
|
Value
LoadXenium
: A Seurat
object
ReadXenium
: A list with some combination of the
following values:
-
“
matrix
”: a sparse matrix with expression data; cells are columns and features are rows -
“
centroids
”: a data frame with cell centroid coordinates in three columns: “x”, “y”, and “cell” -
“
pixels
”: a data frame with molecule pixel coordinates in three columns: “x”, “y”, and “gene”