Persist the coordinate axis convention of a VisiumV2 image

Record whether the centroid column named x represents the horizontal image-column axis or the vertical image-row axis. This does not move coordinates or change the raster. It replaces metadata-based guessing and survives Seurat subsetting and cell renaming. Stored spatial analyses must be rerun after changing the convention.

Usage

SetSpatialImageAxes(
  object,
  image = NULL,
  x_orientation = c("horizontal", "vertical")
)

Arguments

object: A Seurat object.
image: Image name. Required when several images are present.
x_orientation: "horizontal" for custom images whose centroid x is image-column, or "vertical" for Seurat Read10X_Image's positional imagerow/imagecol convention.

Value

A Seurat object with an explicit image coordinate convention.

Examples

data(visium_human_pancreas_sub)
spatial <- SetSpatialImageAxes(
  visium_human_pancreas_sub,
  image = "slice1", x_orientation = "horizontal"
)
SpatialCoordinates(spatial, image = "slice1")$source$coord.cols
#> [1] "x" "y"