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Fix: Remove gobject = named arg from calculateOverlap and overlapToMatrix calls in .createGiottoMerscopeObject_subcellular #1261

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Fix: Remove gobject = named arg from calculateOverlap and overlapToMatrix calls in .createGiottoMerscopeObject_subcellular #1261

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bc8f0d6
Fix calculateOverlap and overlapToMatrix to use positional args
vjarzabek May 22, 2026
29014b0
Fix createMerscopeLargeImage flip message to reflect origin-based flip
vjarzabek May 27, 2026
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17 changes: 9 additions & 8 deletions R/convenience_general.R
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Original file line number Diff line number Diff line change
Expand Up @@ -903,7 +903,7 @@ addVisiumPolygons <- function(gobject,
#' if image_file is a list.
#' @param flip_axis character. Axis along which to reflect the image after the
#' spatial shift: \code{"none"} (default), \code{"y"}, \code{"x"}, or
#' \code{"both"}. The reflection origin is the midpoint of the image extent in
#' \code{"both"}. The reflection is performed around the origin (0, 0) in
#' micron space.
#' @returns giottoLargeImage
#' @export
Expand All @@ -915,11 +915,12 @@ createMerscopeLargeImage <- function(image_file,

if (flip_axis != "none") {
message(
"The image is flipped around its own spatial midpoint (microns).",
" If you also used flip_axis (!= 'none) in createGiottoMerscopeObject,",
" verify that the image aligns with the polygons and transcripts --",
" the flip centers may differ if the image does not cover the same",
" area as the transcript coordinates."
"The image is flipped around the origin (0, 0) in micron space.",
" Note that createGiottoMerscopeObject flips polygons and transcripts",
" around their spatial midpoint, not the origin.",
" If you use flip_axis in both functions, the image and spatial data",
" will likely not align -- consider flipping the image manually after",
" loading to match the flip center of your spatial coordinates."
)
}

Expand Down Expand Up @@ -1284,12 +1285,12 @@ createGiottoMerscopeObject <- function(merscope_dir,
if (isTRUE(verbose)) message("Calculating overlap for polygon layer: ", poly_name)

z_sub <- GiottoClass::calculateOverlap(
gobject = z_sub, spat_info = poly_name, feat_info = "rna"
z_sub, spat_info = poly_name, feat_info = "rna"
)
if (isTRUE(overlap_to_matrix)) {

z_sub <- GiottoClass::overlapToMatrix(
gobject = z_sub, spat_info = poly_name, feat_info = "rna", name = "raw"
z_sub, spat_info = poly_name, feat_info = "rna", name = "raw"
)
}
}
Expand Down