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fix: match Seurat key sanitization when detecting assay-specific reductions #3

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Merged
zqfang merged 1 commit into from
Jul 23, 2026
Merged

fix: match Seurat key sanitization when detecting assay-specific reductions #3

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25 changes: 17 additions & 8 deletions R/WriteH5MU.R
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Original file line number Diff line number Diff line change
Expand Up @@ -158,10 +158,13 @@ WriteH5ADHelper <- function(object, assay, root, scale.data=FALSE, sparse.type="
# This is required since Seurat does require having an existing modality
# in assay.used, which complicates loading multimodal embeddings.
# The latter are currently loaded with the default assay set as assay.used.
if (grepl(tolower(emb_assay), tolower(red_name)) ||
grepl(tolower(emb_assay), tolower(red@key)) ||
grepl(tolower(red_name), tolower(red@key)) ||
grepl(tolower(gsub('\\.', '', red_name)), tolower(red@key))
# Seurat strips non-alphanumeric characters when deriving a key from a
# reduction name (umap_harmony -> umapharmony_), so the name has to be
# sanitized the same way before comparing it against the key.
if (grepl(tolower(emb_assay), tolower(red_name), fixed = TRUE) ||
grepl(tolower(emb_assay), tolower(red@key), fixed = TRUE) ||
grepl(tolower(red_name), tolower(red@key), fixed = TRUE) ||
grepl(tolower(gsub('[^[:alnum:]]', '', red_name)), tolower(red@key), fixed = TRUE)
) {
Comment on lines +164 to 168
modality_specific <- TRUE
}
Expand All @@ -173,6 +176,9 @@ WriteH5ADHelper <- function(object, assay, root, scale.data=FALSE, sparse.type="
}

if (!modality_specific) {
warning(paste0("Reduction ", red_name, " (key ", red@key, ", assay.used ",
emb_assay, ") was not recognised as specific to assay ", assay,
" and will not be written to .obsm."))
next
}

Expand Down Expand Up @@ -406,10 +412,13 @@ setMethod("WriteH5MU", "Seurat", function(object, file, scale.data=FALSE, sparse
# This is required since Seurat does require having an existing modality
# in assay.used, which complicates loading multimodal embeddings.
# The latter are currently loaded with the default assay set as assay.used.
if (grepl(tolower(assay_emb), tolower(red_name)) ||
grepl(tolower(assay_emb), tolower(red@key)) ||
grepl(tolower(red_name), tolower(red@key)) ||
grepl(tolower(gsub('\\.', '', red_name)), tolower(red@key))
# Seurat strips non-alphanumeric characters when deriving a key from a
# reduction name (umap_harmony -> umapharmony_), so the name has to be
# sanitized the same way before comparing it against the key.
if (grepl(tolower(assay_emb), tolower(red_name), fixed = TRUE) ||
grepl(tolower(assay_emb), tolower(red@key), fixed = TRUE) ||
grepl(tolower(red_name), tolower(red@key), fixed = TRUE) ||
grepl(tolower(gsub('[^[:alnum:]]', '', red_name)), tolower(red@key), fixed = TRUE)
) {
modality_specific <- TRUE
}
Expand Down