Read and Load 10x Genomics Xenium in-situ data
LoadXenium(data.dir, fov = "fov", assay = "Xenium")ReadXenium(
data.dir,
outs = c("matrix", "microns"),
type = "centroids",
mols.qv.threshold = 20
)
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
Types of molecular outputs to read; choose one or more of:
“matrix”: the counts matrix
“microns”: molecule coordinates
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
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.