Read and Load 10x Genomics Xenium in-situ data
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
)
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”
Directory containing all Xenium output files with default filenames
FOV name
Assay name
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.
Whether or not to load cell centroids
Whether or not to load molecule pixel coordinates
One of "cell", "nucleus" or NULL (to load either cell segmentations, nucleus segmentations or neither)
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.
Types of molecular outputs to read; choose one or more of:
“matrix”: the counts matrix
“microns”: molecule coordinates
“segmentation_method”: cell segmentation method (for runs which use multi-modal segmentation)
Type of cell spatial coordinate matrices to read; choose one or more of:
“centroids”: cell centroids in pixel coordinate space
“segmentations”: cell segmentations in pixel coordinate space
“nucleus_segmentations”: nucleus segmentations in pixel coordinate space