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Merge pull request #1304 from AlexsLemonade/allyhawkins/merged-formatting-reference
Add merged object information to reference SCE and AnnData files
2 parents 0fe77c9 + 587d087 commit c209402

3 files changed

Lines changed: 462 additions & 18 deletions

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‎references/anndata-formatting-reference.json‎

Lines changed: 173 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -13,10 +13,10 @@
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"subsets_mito_detected": "int",
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"subsets_mito_percent": "float",
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"total": "float",
16-
"library_id": "category",
17-
"sample_id": "category",
18-
"assay_ontology_term_id": "category",
19-
"suspension_type": "category",
16+
"library_id": "string",
17+
"sample_id": "string",
18+
"assay_ontology_term_id": "string",
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"suspension_type": "string",
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"is_primary_data": "bool"
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},
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"var": {
@@ -110,10 +110,10 @@
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"scpca_filter": "string",
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"scDblFinder_class": "string",
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"scDblFinder_score": "float",
113-
"library_id": "category",
114-
"sample_id": "category",
115-
"assay_ontology_term_id": "category",
116-
"suspension_type": "category",
113+
"library_id": "string",
114+
"sample_id": "string",
115+
"assay_ontology_term_id": "string",
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"suspension_type": "string",
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"is_primary_data": "bool"
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},
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"var": {
@@ -258,10 +258,10 @@
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"scpca_filter": "string",
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"scDblFinder_class": "string",
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"scDblFinder_score": "float",
261-
"library_id": "category",
262-
"sample_id": "category",
263-
"assay_ontology_term_id": "category",
264-
"suspension_type": "category",
261+
"library_id": "string",
262+
"sample_id": "string",
263+
"assay_ontology_term_id": "string",
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"suspension_type": "string",
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"is_primary_data": "bool"
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},
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"var": {
@@ -459,5 +459,166 @@
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"ambient_profile": "float"
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}
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}
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},
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"merged": {
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"rna": {
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"has_raw.X": true,
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"layers": [
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"spliced"
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],
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"obs": {
470+
"barcodes": "string",
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"sum": "float",
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"detected": "int",
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"subsets_mito_sum": "float",
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"subsets_mito_detected": "int",
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"subsets_mito_percent": "float",
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"total": "float",
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"prob_compromised": "float",
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"miQC_pass": "bool",
479+
"scpca_filter": "string",
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"scDblFinder_class": "string",
481+
"scDblFinder_score": "float",
482+
"additional_modalities": "string",
483+
"library_id": "string",
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"cell_id": "string",
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"sample_id": "string",
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"scpca_project_id": "string",
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"submitter_id": "string",
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"participant_id": "string",
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"submitter": "string",
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"age": "string",
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"age_timing": "string",
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"sex": "string",
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"diagnosis": "string",
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"subdiagnosis": "string",
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"tissue_location": "string",
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"disease_timing": "string",
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"organism": "string",
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"is_xenograft": "bool",
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"is_cell_line": "bool",
500+
"development_stage_ontology_term_id": "string",
501+
"sex_ontology_term_id": "string",
502+
"organism_ontology_term_id": "string",
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"self_reported_ethnicity_ontology_term_id": "string",
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"disease_ontology_term_id": "string",
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"tissue_ontology_term_id": "string",
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"tech_version": "string",
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"assay_ontology_term_id": "string",
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"suspension_type": "string",
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"is_primary_data": "bool"
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},
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"var": {
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"gene_ids": "string",
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"gene_symbol": "string",
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"mean": "float",
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"detected": "float",
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"feature_is_filtered": "bool",
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"highly_variable": "bool"
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},
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"obs_conditional": {
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"has_submitter": {
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"submitter_celltype_annotation": "string"
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},
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"has_openscpca": {
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"openscpca_celltype_annotation": "string",
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"openscpca_celltype_ontology": "string"
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},
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"has_adt": {
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"adt_scpca_filter": "string"
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},
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"has_cellhash": {
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"altexps_cellhash_sum": "float",
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"altexps_cellhash_detected": "int",
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"altexps_cellhash_percent": "float"
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},
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"has_hashedDrops": {
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"hashedDrops_sampleid": "string"
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},
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"has_HTODemux": {
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"HTODemux_sampleid": "string"
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},
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"has_vireo": {
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"vireo_sampleid": "string",
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"vireo_donor_id": "string",
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"vireo_prob_max": "float",
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"vireo_prob_doublet": "float",
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"vireo_n_vars": "float",
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"vireo_best_singlet": "string",
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"vireo_best_doublet": "string",
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"vireo_doublet_logLikRatio": "float"
550+
},
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"has_normalization": {
552+
"sizeFactor": "float"
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},
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"has_clusters": {
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"cluster": "category"
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},
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"has_singler": {
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"singler_celltype_annotation": "string",
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"singler_celltype_ontology": "string"
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},
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"has_cellassign": {
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"cellassign_celltype_annotation": "string",
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"cellassign_celltype_ontology": "string",
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"cellassign_max_prediction": "float"
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},
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"has_scimilarity": {
567+
"scimilarity_celltype_annotation": "string",
568+
"scimilarity_celltype_ontology": "string",
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"scimilarity_min_distance": "float"
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},
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"has_consensus": {
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"consensus_celltype_annotation": "string",
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"consensus_celltype_ontology": "string"
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},
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"has_infercnv": {
576+
"is_infercnv_reference": "bool",
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"infercnv_total_cnv": "int"
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},
579+
"is_multiplexed": {
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"sample_id": null
581+
}
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},
583+
"obsm": [
584+
"X_pca",
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"X_umap"
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],
587+
"uns": {
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"library_id": "string",
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"sample_id": "string",
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"merged_highly_variable_genes": "string"
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}
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},
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"adt": {
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"obs": {
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"zero.ambient": "bool",
596+
"discard": "bool",
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"library_id": "string",
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"cell_id": "string"
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},
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"var": {
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"adt_id": "string",
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"mean": "float",
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"detected": "float",
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"target_type": "string"
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},
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"obs_conditional": {
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"has_negative_control": {
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"sum.controls": "int",
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"high.control": "bool"
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},
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"no_negative_control": {
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"ambient.scale": "float",
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"high.ambient": "bool"
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},
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"sizeFactor": "float"
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},
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"uns": {
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"library_id": "string",
619+
"sample_id": "string",
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"library_metadata": "string"
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}
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}
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}
463624
}

‎references/sce-formatting-reference.json‎

Lines changed: 162 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -319,7 +319,8 @@
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"processed": {
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"assayNames": [
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"counts",
322-
"spliced"
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"spliced",
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"logcounts"
323324
],
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"colData": {
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"barcodes": "character",
@@ -575,5 +576,165 @@
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}
576577
}
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}
579+
},
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"merged": {
581+
"assayNames": [
582+
"counts",
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"spliced",
584+
"logcounts"
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],
586+
"colData": {
587+
"barcodes": "character",
588+
"sum": "numeric",
589+
"detected": "numeric",
590+
"subsets_mito_sum": "numeric",
591+
"subsets_mito_detected": "integer",
592+
"subsets_mito_percent": "numeric",
593+
"total": "numeric",
594+
"prob_compromised": "numeric",
595+
"miQC_pass": "logical",
596+
"scpca_filter": "character",
597+
"scDblFinder_class": "character",
598+
"scDblFinder_score": "numeric",
599+
"additional_modalities": "character",
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"library_id": "character",
601+
"cell_id": "character",
602+
"sample_id": "character",
603+
"scpca_project_id": "character",
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"submitter_id": "character",
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"participant_id": "character",
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"submitter": "character",
607+
"age": "character",
608+
"age_timing": "character",
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"sex": "character",
610+
"diagnosis": "character",
611+
"subdiagnosis": "character",
612+
"tissue_location": "character",
613+
"disease_timing": "character",
614+
"organism": "character",
615+
"is_xenograft": "logical",
616+
"is_cell_line": "logical",
617+
"development_stage_ontology_term_id": "character",
618+
"sex_ontology_term_id": "character",
619+
"organism_ontology_term_id": "character",
620+
"self_reported_ethnicity_ontology_term_id": "character",
621+
"disease_ontology_term_id": "character",
622+
"tissue_ontology_term_id": "character",
623+
"tech_version": "character",
624+
"assay_ontology_term_id": "character",
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"suspension_type": "character"
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},
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"rowData": {
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"gene_ids": "character",
629+
"gene_symbol": "character",
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"mean": "numeric",
631+
"detected": "numeric"
632+
},
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"colData_conditional": {
634+
"has_submitter": {
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"submitter_celltype_annotation": "character"
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},
637+
"has_openscpca": {
638+
"openscpca_celltype_annotation": "character",
639+
"openscpca_celltype_ontology": "character"
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},
641+
"has_adt": {
642+
"adt_scpca_filter": "character"
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},
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"has_cellhash": {
645+
"altexps_cellhash_sum": "numeric",
646+
"altexps_cellhash_detected": "integer",
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"altexps_cellhash_percent": "numeric"
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},
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"has_hashedDrops": {
650+
"hashedDrops_sampleid": "character"
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},
652+
"has_HTODemux": {
653+
"HTODemux_sampleid": "character"
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},
655+
"has_vireo": {
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"vireo_sampleid": "character",
657+
"vireo_donor_id": "character",
658+
"vireo_prob_max": "numeric",
659+
"vireo_prob_doublet": "numeric",
660+
"vireo_n_vars": "numeric",
661+
"vireo_best_singlet": "character",
662+
"vireo_best_doublet": "character",
663+
"vireo_doublet_logLikRatio": "numeric"
664+
},
665+
"has_normalization": {
666+
"sizeFactor": "numeric"
667+
},
668+
"has_clusters": {
669+
"cluster": "factor"
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},
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"has_singler": {
672+
"singler_celltype_annotation": "character",
673+
"singler_celltype_ontology": "character"
674+
},
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"has_cellassign": {
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"cellassign_celltype_annotation": "character",
677+
"cellassign_celltype_ontology": "character",
678+
"cellassign_max_prediction": "numeric"
679+
},
680+
"has_scimilarity": {
681+
"scimilarity_celltype_annotation": "character",
682+
"scimilarity_celltype_ontology": "character",
683+
"scimilarity_min_distance": "numeric"
684+
},
685+
"has_consensus": {
686+
"consensus_celltype_annotation": "character",
687+
"consensus_celltype_ontology": "character"
688+
},
689+
"has_infercnv": {
690+
"is_infercnv_reference": "logical",
691+
"infercnv_total_cnv": "integer"
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}
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},
694+
"reducedDimNames": [
695+
"PCA",
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"UMAP"
697+
],
698+
"metadata": {
699+
"library_id": "character",
700+
"sample_id": "character",
701+
"library_metadata": "list",
702+
"merged_highly_variable_genes": "character"
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},
704+
"altExp": {
705+
"adt": {
706+
"assayNames": [
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"counts"
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],
709+
"colData": {
710+
"zero.ambient": "logical",
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"discard": "logical",
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"library_id": "character",
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"cell_id": "character"
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},
715+
"rowData": {
716+
"adt_id": "character",
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"mean": "numeric",
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"detected": "numeric",
719+
"target_type": "character"
720+
},
721+
"colData_conditional": {
722+
"has_negative_control": {
723+
"sum.controls": "integer",
724+
"high.control": "logical"
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},
726+
"no_negative_control": {
727+
"ambient.scale": "numeric",
728+
"high.ambient": "logical"
729+
},
730+
"sizeFactor": "numeric"
731+
},
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"metadata": {
733+
"library_id": "character",
734+
"sample_id": "character",
735+
"library_metadata": "list"
736+
}
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}
738+
}
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}
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}

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