ReadXenium: Read and Load 10x Genomics Xenium in-situ data
In satijalab/seurat: Tools for Single Cell Genomics

LoadXenium

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: “matrix”: the counts matrix “microns”: molecule coordinates “segmentation_method”: cell segmentation method (for runs which use multi-modal segmentation)
`type`	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

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”