diff --git a/R/convenience_xenium.R b/R/convenience_xenium.R index 6fb8bc4ad..931ce3fa0 100644 --- a/R/convenience_xenium.R +++ b/R/convenience_xenium.R @@ -487,7 +487,8 @@ setMethod( path = metadata_path, verbose = verbose ) - g <- setGiotto(g, cx) + # verbose = FALSE to silence warning that meta is already generated + g <- setGiotto(g, cx, verbose = FALSE) } @@ -553,12 +554,15 @@ setMethod( } # centroids + vmsg(.v = verbose, "calculating centroids") spat_units_to_calc <- list_spatial_info_names(g) g <- addSpatialCentroidLocations(g, poly_info = spat_units_to_calc, provenance = as.list(spat_units_to_calc), verbose = FALSE ) + + vmsg(.v = verbose, "done") return(g) } diff --git a/man/createGiottoXeniumObject.Rd b/man/createGiottoXeniumObject.Rd index f803aece8..5f41859b8 100644 --- a/man/createGiottoXeniumObject.Rd +++ b/man/createGiottoXeniumObject.Rd @@ -14,8 +14,9 @@ createGiottoXeniumObject( feat_type = c("rna", "NegControlProbe", "UnassignedCodeword", "NegControlCodeword"), split_keyword = list("NegControlProbe", "UnassignedCodeword", "NegControlCodeword"), qv_threshold = 20, - load_images = NULL, + load_images = "focus", load_aligned_images = NULL, + load_transcripts = TRUE, load_expression = FALSE, load_cellmeta = FALSE, instructions = NULL,