Load 10X Genomics Visium Cell Segmentations

Usage

Read10X_Segmentations(
  image.dir,
  data.dir,
  image.name = "tissue_lowres_image.png",
  assay = "Spatial.Polygons",
  slice = "slice1.polygons",
  segmentation.type = "cell",
  compact = TRUE,
  cells = NULL
)

Arguments

image.dir: Path to directory with 10X Genomics visium image data;
data.dir: Directory of the base spaceranger outs
image.name: Name of the tissue image to be plotted. tissue_lowres_image.png or tissue_hires_image.png
assay: Name of assay to associate segmentations to
slice: Name of the slice to associate the segmentations to
segmentation.type: Which segmentations to load, cell or nucleus. If using nucleus the full matrix from cells is still used
compact: Whether to store segmentations in only the sf.data slot in the corresponding Segmentation object (default TRUE) to save memory and processing time. If FALSE, segmentations are also stored in sp format in addition to the sf.data slot.
cells: Optional vector of cell barcodes to retain.

Value

A VisiumV2 object with segmentations