Trim spots/bins from the edges of a Visium (or VisiumHD) slide

Removes whole lines of spots from the outer edges of an aligned Visium or VisiumHD array, using the regular array_row/array_col grid. Useful for quickly shaving off edge artefacts (folds, tears, capture effects).

Usage

trimEdge(spe, trim = c(0, 0, 0, 0))

Arguments

spe

A SpatialExperiment with array_row and array_col in its colData.

trim

Integer vector of length 4 giving the number of spot lines to remove from each edge, in the order c(bottom, left, top, right) (the base R par mar order). Default c(0, 0, 0, 0) (no trimming).

Value

The SpatialExperiment with the edge spots removed.

Details

Edges are defined in the stored-coordinate frame, which is independent of any plotting choice: left = smallest x, right = largest x, top = smallest y, bottom = largest y. This matches the orientation of scider's default image plot (which is Y-reversed). Note that a plot drawn without the Y-reversal (e.g. an object read without an image, or reverseY = FALSE) is vertically mirrored, so top then appears at the bottom of that plot.

Trimming removes the n smallest/largest array_col values (for left/right) and array_row values (for top/ bottom). Because of the Visium hexagonal offset, one array_col value spans only alternate rows, so removing a single value trims roughly half a visual column at a time; use 2 for a full column line. array_row values are clean horizontal lines. VisiumHD's square grid has no such half-offset.

This function requires array_row/array_col in colData(spe) and therefore only applies to Visium/VisiumHD.

Examples

if (FALSE) { # \dontrun{
spe <- readVisium("path/to/visium/outs")
# 1 line off the bottom, 2 off the left, 3 off the top, 4 off the right
spe <- trimEdge(spe, trim = c(1, 2, 3, 4))
} # }