@vitessce/constants-internal 3.5.7 → 3.5.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (14) hide show
  1. package/dist/index.js +140 -5
  2. package/dist-tsc/constant-relationships.d.ts.map +1 -1
  3. package/dist-tsc/constant-relationships.js +36 -0
  4. package/dist-tsc/constants.d.ts +29 -0
  5. package/dist-tsc/constants.d.ts.map +1 -1
  6. package/dist-tsc/constants.js +30 -0
  7. package/dist-tsc/coordination.d.ts.map +1 -1
  8. package/dist-tsc/coordination.js +69 -0
  9. package/dist-tsc/version.json +3 -3
  10. package/package.json +1 -1
  11. package/src/constant-relationships.ts +37 -0
  12. package/src/constants.ts +35 -0
  13. package/src/coordination.ts +69 -0
  14. package/src/version.json +3 -3
package/dist/index.js CHANGED
@@ -16,8 +16,13 @@ const ViewType = {
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  FEATURE_VALUE_HISTOGRAM: "featureValueHistogram",
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  DOT_PLOT: "dotPlot",
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  FEATURE_BAR_PLOT: "featureBarPlot",
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+ VOLCANO_PLOT: "volcanoPlot",
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+ OBS_SET_COMPOSITION_BAR_PLOT: "obsSetCompositionBarPlot",
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+ FEATURE_SET_ENRICHMENT_BAR_PLOT: "featureSetEnrichmentBarPlot",
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  BIOMARKER_SELECT: "biomarkerSelect",
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+ COMPARATIVE_HEADING: "comparativeHeading",
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  LINK_CONTROLLER: "linkController",
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+ NEUROGLANCER: "neuroglancer",
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  DUAL_SCATTERPLOT: "dualScatterplot",
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  TREEMAP: "treemap"
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  };
@@ -35,7 +40,11 @@ const DataType = {
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  OBS_POINTS: "obsPoints",
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  OBS_LOCATIONS: "obsLocations",
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  SAMPLE_SETS: "sampleSets",
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- SAMPLE_EDGES: "sampleEdges"
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+ SAMPLE_EDGES: "sampleEdges",
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+ COMPARISON_METADATA: "comparisonMetadata",
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+ FEATURE_STATS: "featureStats",
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+ FEATURE_SET_STATS: "featureSetStats",
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+ OBS_SET_STATS: "obsSetStats"
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  };
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  const AsyncFunctionType = {
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  // String input (rather than Node input)
@@ -96,6 +105,10 @@ const FileType = {
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  FEATURE_LABELS_ANNDATA_ZARR: "featureLabels.anndata.zarr",
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  SAMPLE_EDGES_ANNDATA_ZARR: "sampleEdges.anndata.zarr",
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  SAMPLE_SETS_ANNDATA_ZARR: "sampleSets.anndata.zarr",
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+ COMPARISON_METADATA_ANNDATA_ZARR: "comparisonMetadata.anndata.zarr",
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+ COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR: "comparativeFeatureStats.anndata.zarr",
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+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR: "comparativeFeatureSetStats.anndata.zarr",
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+ COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR: "comparativeObsSetStats.anndata.zarr",
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  // AnnData - zipped
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  OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: "obsFeatureMatrix.anndata.zarr.zip",
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  OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: "obsFeatureColumns.anndata.zarr.zip",
@@ -109,6 +122,10 @@ const FileType = {
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  FEATURE_LABELS_ANNDATA_ZARR_ZIP: "featureLabels.anndata.zarr.zip",
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  SAMPLE_EDGES_ANNDATA_ZARR_ZIP: "sampleEdges.anndata.zarr.zip",
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  SAMPLE_SETS_ANNDATA_ZARR_ZIP: "sampleSets.anndata.zarr.zip",
125
+ COMPARISON_METADATA_ANNDATA_ZARR_ZIP: "comparisonMetadata.anndata.zarr.zip",
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+ COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR_ZIP: "comparativeFeatureStats.anndata.zarr.zip",
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+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR_ZIP: "comparativeFeatureSetStats.anndata.zarr.zip",
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+ COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR_ZIP: "comparativeObsSetStats.anndata.zarr.zip",
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  // AnnData - h5ad via reference spec
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  OBS_FEATURE_MATRIX_ANNDATA_H5AD: "obsFeatureMatrix.anndata.h5ad",
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  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: "obsFeatureColumns.anndata.h5ad",
@@ -122,6 +139,10 @@ const FileType = {
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  FEATURE_LABELS_ANNDATA_H5AD: "featureLabels.anndata.h5ad",
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  SAMPLE_EDGES_ANNDATA_H5AD: "sampleEdges.anndata.h5ad",
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  SAMPLE_SETS_ANNDATA_H5AD: "sampleSets.anndata.h5ad",
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+ COMPARISON_METADATA_ANNDATA_H5AD: "comparisonMetadata.anndata.h5ad",
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+ COMPARATIVE_FEATURE_STATS_ANNDATA_H5AD: "comparativeFeatureStats.anndata.h5ad",
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+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_H5AD: "comparativeFeatureSetStats.anndata.h5ad",
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+ COMPARATIVE_OBS_SET_STATS_ANNDATA_H5AD: "comparativeObsSetStats.anndata.h5ad",
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  // SpatialData
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  IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
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  LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
@@ -320,6 +341,11 @@ const CoordinationType = {
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  EMBEDDING_CONTOUR_PERCENTILES: "embeddingContourPercentiles",
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  CONTOUR_COLOR_ENCODING: "contourColorEncoding",
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  CONTOUR_COLOR: "contourColor",
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+ // For volcano plot:
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+ FEATURE_POINT_SIGNIFICANCE_THRESHOLD: "featurePointSignificanceThreshold",
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+ FEATURE_LABEL_SIGNIFICANCE_THRESHOLD: "featureLabelSignificanceThreshold",
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+ FEATURE_POINT_FOLD_CHANGE_THRESHOLD: "featurePointFoldChangeThreshold",
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+ FEATURE_LABEL_FOLD_CHANGE_THRESHOLD: "featureLabelFoldChangeThreshold",
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  // Treemap
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  HIERARCHY_LEVELS: "hierarchyLevels"
325
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  };
@@ -348,7 +374,11 @@ const ViewHelpMapping = {
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  FEATURE_VALUE_HISTOGRAM: "The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).",
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  DOT_PLOT: "The dot plot displays summary information about expression of the selected features (e.g., genes) for each selected observation set (e.g., cell type).",
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  FEATURE_BAR_PLOT: "The feature bar plot displays one bar per observation (e.g., cell) along the x-axis, where the value of a selected feature (e.g., gene) is encoded along the y-axis.",
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- TREEMAP: "The treemap provides an overview of the current state of sample-level or cell-level selection and filtering."
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+ NEUROGLANCER: "The Neuroglancer view displays 3d meshes using Neuroglancer developed by Google.",
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+ TREEMAP: "The treemap provides an overview of the current state of sample-level or cell-level selection and filtering.",
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+ VOLCANO_PLOT: "The volcano plot displays differential expression results. Each data point represents a feature (as opposed to an observation).",
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+ OBS_SET_COMPOSITION_BAR_PLOT: "The set composition bar plot displays the results of a compositional analysis conducted using the scCODA method (Büttner et al. 2021 Nature Communications).",
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+ FEATURE_SET_ENRICHMENT_BAR_PLOT: "The feature set enrichment bar plot displays the results of a hypergeometric test applied to the differential expression test results to identify enriched pathway gene sets."
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  };
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  const FILE_TYPE_DATA_TYPE_MAPPING = {
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  // For new file types
@@ -377,6 +407,10 @@ const FILE_TYPE_DATA_TYPE_MAPPING = {
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  [FileType.FEATURE_LABELS_ANNDATA_ZARR]: DataType.FEATURE_LABELS,
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  [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: DataType.SAMPLE_EDGES,
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  [FileType.SAMPLE_SETS_ANNDATA_ZARR]: DataType.SAMPLE_SETS,
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+ [FileType.COMPARISON_METADATA_ANNDATA_ZARR]: DataType.COMPARISON_METADATA,
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+ [FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR]: DataType.FEATURE_STATS,
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+ [FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR]: DataType.FEATURE_SET_STATS,
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+ [FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR]: DataType.OBS_SET_STATS,
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  [FileType.IMAGE_OME_TIFF]: DataType.IMAGE,
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  [FileType.OBS_SEGMENTATIONS_OME_TIFF]: DataType.OBS_SEGMENTATIONS,
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  [FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
@@ -457,6 +491,22 @@ const DATA_TYPE_COORDINATION_VALUE_USAGE = {
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  [DataType.SAMPLE_EDGES]: [
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  CoordinationType.OBS_TYPE,
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  CoordinationType.SAMPLE_TYPE
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+ ],
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+ [DataType.COMPARISON_METADATA]: [
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+ CoordinationType.OBS_TYPE,
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+ CoordinationType.SAMPLE_TYPE
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+ ],
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+ [DataType.FEATURE_STATS]: [
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+ CoordinationType.FEATURE_TYPE
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+ // TODO: should sampleType, obsSetSelection, and/or sampleSetSelection be used here?
502
+ ],
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+ [DataType.FEATURE_SET_STATS]: [
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+ CoordinationType.FEATURE_TYPE
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+ // TODO: should sampleType, obsSetSelection, and/or sampleSetSelection be used here?
506
+ ],
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+ [DataType.OBS_SET_STATS]: [
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+ CoordinationType.OBS_TYPE
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+ // TODO: should sampleType, obsSetSelection, and/or sampleSetSelection be used here?
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  ]
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  };
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  const ALT_ZARR_STORE_TYPES = {
@@ -509,6 +559,22 @@ const ALT_ZARR_STORE_TYPES = {
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  zip: FileType.SAMPLE_SETS_ANNDATA_ZARR_ZIP,
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  h5ad: FileType.SAMPLE_SETS_ANNDATA_H5AD
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  },
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+ [FileType.COMPARISON_METADATA_ANNDATA_ZARR]: {
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+ zip: FileType.COMPARISON_METADATA_ANNDATA_ZARR_ZIP,
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+ h5ad: FileType.COMPARISON_METADATA_ANNDATA_H5AD
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+ },
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+ [FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR]: {
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+ zip: FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR_ZIP,
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+ h5ad: FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_H5AD
569
+ },
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+ [FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR]: {
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+ zip: FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR_ZIP,
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+ h5ad: FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_H5AD
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+ },
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+ [FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR]: {
575
+ zip: FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR_ZIP,
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+ h5ad: FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_H5AD
577
+ },
512
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  // For OME-Zarr:
513
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  [FileType.IMAGE_OME_ZARR]: {
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  zip: FileType.IMAGE_OME_ZARR_ZIP
@@ -533,6 +599,9 @@ const AUTO_INDEPENDENT_COORDINATION_TYPES = [
533
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  CoordinationType.EMBEDDING_OBS_OPACITY
534
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  ];
535
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  const COMPONENT_COORDINATION_TYPES = {
602
+ [ViewType.NEUROGLANCER]: [
603
+ CoordinationType.DATASET
604
+ ],
536
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  [ViewType.SCATTERPLOT]: [
537
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  CoordinationType.DATASET,
538
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  CoordinationType.OBS_TYPE,
@@ -1002,8 +1071,64 @@ const COMPONENT_COORDINATION_TYPES = {
1002
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  CoordinationType.OBS_COLOR_ENCODING,
1003
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  CoordinationType.ADDITIONAL_OBS_SETS
1004
1073
  ],
1074
+ [ViewType.VOLCANO_PLOT]: [
1075
+ CoordinationType.DATASET,
1076
+ CoordinationType.OBS_TYPE,
1077
+ CoordinationType.FEATURE_TYPE,
1078
+ CoordinationType.SAMPLE_TYPE,
1079
+ // For selection of case-control sets of samples:
1080
+ CoordinationType.SAMPLE_SET_SELECTION,
1081
+ // For selection of one-vs-others sets of observations:
1082
+ CoordinationType.OBS_SET_SELECTION,
1083
+ // TODO: CoordinationType.FEATURE_SET_SELECTION,
1084
+ // TODO: CoordinationType.FEATURE_SET_HIGHLIGHT,
1085
+ // TODO: CoordinationType.FEATURE_SET_COLOR,
1086
+ CoordinationType.FEATURE_HIGHLIGHT,
1087
+ CoordinationType.FEATURE_SELECTION,
1088
+ CoordinationType.FEATURE_VALUE_COLORMAP,
1089
+ CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
1090
+ // TODO: CoordinationType.FEATURE_COLOR_ENCODING,
1091
+ // TODO: CoordinationType.ADDITIONAL_FEATURE_SETS,
1092
+ CoordinationType.TOOLTIPS_VISIBLE,
1093
+ CoordinationType.ADDITIONAL_OBS_SETS,
1094
+ CoordinationType.OBS_SET_COLOR,
1095
+ CoordinationType.SAMPLE_SET_COLOR,
1096
+ CoordinationType.FEATURE_POINT_SIGNIFICANCE_THRESHOLD,
1097
+ CoordinationType.FEATURE_LABEL_SIGNIFICANCE_THRESHOLD,
1098
+ CoordinationType.FEATURE_POINT_FOLD_CHANGE_THRESHOLD,
1099
+ CoordinationType.FEATURE_LABEL_FOLD_CHANGE_THRESHOLD
1100
+ ],
1101
+ [ViewType.OBS_SET_COMPOSITION_BAR_PLOT]: [
1102
+ CoordinationType.DATASET,
1103
+ CoordinationType.OBS_TYPE,
1104
+ CoordinationType.SAMPLE_TYPE,
1105
+ // For selection of case-control sets of samples:
1106
+ CoordinationType.SAMPLE_SET_SELECTION,
1107
+ // For selection of one-vs-others sets of observations:
1108
+ CoordinationType.OBS_SET_SELECTION,
1109
+ CoordinationType.ADDITIONAL_OBS_SETS,
1110
+ CoordinationType.OBS_SET_COLOR,
1111
+ CoordinationType.SAMPLE_SET_COLOR
1112
+ ],
1113
+ [ViewType.FEATURE_SET_ENRICHMENT_BAR_PLOT]: [
1114
+ CoordinationType.DATASET,
1115
+ CoordinationType.OBS_TYPE,
1116
+ CoordinationType.FEATURE_TYPE,
1117
+ CoordinationType.SAMPLE_TYPE,
1118
+ // For selection of case-control sets of samples:
1119
+ CoordinationType.SAMPLE_SET_SELECTION,
1120
+ // For selection of one-vs-others sets of observations:
1121
+ CoordinationType.OBS_SET_SELECTION,
1122
+ CoordinationType.ADDITIONAL_OBS_SETS,
1123
+ CoordinationType.OBS_SET_COLOR,
1124
+ CoordinationType.SAMPLE_SET_COLOR,
1125
+ CoordinationType.FEATURE_SELECTION
1126
+ ],
1005
1127
  [ViewType.LINK_CONTROLLER]: [],
1006
1128
  [ViewType.BIOMARKER_SELECT]: [
1129
+ CoordinationType.DATASET,
1130
+ CoordinationType.OBS_TYPE,
1131
+ CoordinationType.SAMPLE_TYPE,
1007
1132
  CoordinationType.FEATURE_SELECTION,
1008
1133
  CoordinationType.SAMPLE_SET_SELECTION,
1009
1134
  CoordinationType.SAMPLE_SET_FILTER,
@@ -1011,6 +1136,16 @@ const COMPONENT_COORDINATION_TYPES = {
1011
1136
  CoordinationType.OBS_SET_FILTER
1012
1137
  // TODO: create coordination types for internal state of the biomarker selection view?
1013
1138
  ],
1139
+ [ViewType.COMPARATIVE_HEADING]: [
1140
+ CoordinationType.DATASET,
1141
+ CoordinationType.OBS_TYPE,
1142
+ CoordinationType.SAMPLE_TYPE,
1143
+ CoordinationType.FEATURE_SELECTION,
1144
+ CoordinationType.SAMPLE_SET_SELECTION,
1145
+ CoordinationType.SAMPLE_SET_FILTER,
1146
+ CoordinationType.OBS_SET_SELECTION,
1147
+ CoordinationType.OBS_SET_FILTER
1148
+ ],
1014
1149
  [ViewType.TREEMAP]: [
1015
1150
  CoordinationType.DATASET,
1016
1151
  CoordinationType.OBS_TYPE,
@@ -1039,10 +1174,10 @@ const COMPONENT_COORDINATION_TYPES = {
1039
1174
  ]
1040
1175
  };
1041
1176
  const note = "This file is autogenerated by .changeset/post-changelog.mjs.";
1042
- const version = "3.5.7";
1043
- const date = "2025-02-19";
1177
+ const version = "3.5.8";
1178
+ const date = "2025-03-06";
1044
1179
  const branch = "changeset-release/main";
1045
- const hash = "a4bc3a6a";
1180
+ const hash = "9066c55a";
1046
1181
  const version$1 = {
1047
1182
  note,
1048
1183
  version,
package/dist-tsc/constant-relationships.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"constant-relationships.d.ts","sourceRoot":"","sources":["../src/constant-relationships.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AACH,eAAO,MAAM,2BAA2B;;CAgEvC,CAAC;AAEF;;;;GAIG;AACH,eAAO,MAAM,kCAAkC;;CA6C9C,CAAC;AAKF,eAAO,MAAM,oBAAoB;;;;;;;;CAyDhC,CAAC"}
1
+ {"version":3,"file":"constant-relationships.d.ts","sourceRoot":"","sources":["../src/constant-relationships.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AACH,eAAO,MAAM,2BAA2B;;CAoEvC,CAAC;AAEF;;;;GAIG;AACH,eAAO,MAAM,kCAAkC;;CA6D9C,CAAC;AAKF,eAAO,MAAM,oBAAoB;;;;;;;;CA0EhC,CAAC"}
package/dist-tsc/constant-relationships.js CHANGED
@@ -31,6 +31,10 @@ export const FILE_TYPE_DATA_TYPE_MAPPING = {
31
31
  [FileType.FEATURE_LABELS_ANNDATA_ZARR]: DataType.FEATURE_LABELS,
32
32
  [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: DataType.SAMPLE_EDGES,
33
33
  [FileType.SAMPLE_SETS_ANNDATA_ZARR]: DataType.SAMPLE_SETS,
34
+ [FileType.COMPARISON_METADATA_ANNDATA_ZARR]: DataType.COMPARISON_METADATA,
35
+ [FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR]: DataType.FEATURE_STATS,
36
+ [FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR]: DataType.FEATURE_SET_STATS,
37
+ [FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR]: DataType.OBS_SET_STATS,
34
38
  [FileType.IMAGE_OME_TIFF]: DataType.IMAGE,
35
39
  [FileType.OBS_SEGMENTATIONS_OME_TIFF]: DataType.OBS_SEGMENTATIONS,
36
40
  [FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
@@ -117,6 +121,22 @@ export const DATA_TYPE_COORDINATION_VALUE_USAGE = {
117
121
  CoordinationType.OBS_TYPE,
118
122
  CoordinationType.SAMPLE_TYPE,
119
123
  ],
124
+ [DataType.COMPARISON_METADATA]: [
125
+ CoordinationType.OBS_TYPE,
126
+ CoordinationType.SAMPLE_TYPE,
127
+ ],
128
+ [DataType.FEATURE_STATS]: [
129
+ CoordinationType.FEATURE_TYPE,
130
+ // TODO: should sampleType, obsSetSelection, and/or sampleSetSelection be used here?
131
+ ],
132
+ [DataType.FEATURE_SET_STATS]: [
133
+ CoordinationType.FEATURE_TYPE,
134
+ // TODO: should sampleType, obsSetSelection, and/or sampleSetSelection be used here?
135
+ ],
136
+ [DataType.OBS_SET_STATS]: [
137
+ CoordinationType.OBS_TYPE,
138
+ // TODO: should sampleType, obsSetSelection, and/or sampleSetSelection be used here?
139
+ ],
120
140
  };
121
141
  // For Zarr-based file types, we keep a mapping to file types
122
142
  // corresponding to alternative store implementations,
@@ -171,6 +191,22 @@ export const ALT_ZARR_STORE_TYPES = {
171
191
  zip: FileType.SAMPLE_SETS_ANNDATA_ZARR_ZIP,
172
192
  h5ad: FileType.SAMPLE_SETS_ANNDATA_H5AD,
173
193
  },
194
+ [FileType.COMPARISON_METADATA_ANNDATA_ZARR]: {
195
+ zip: FileType.COMPARISON_METADATA_ANNDATA_ZARR_ZIP,
196
+ h5ad: FileType.COMPARISON_METADATA_ANNDATA_H5AD,
197
+ },
198
+ [FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR]: {
199
+ zip: FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR_ZIP,
200
+ h5ad: FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_H5AD,
201
+ },
202
+ [FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR]: {
203
+ zip: FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR_ZIP,
204
+ h5ad: FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_H5AD,
205
+ },
206
+ [FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR]: {
207
+ zip: FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR_ZIP,
208
+ h5ad: FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_H5AD,
209
+ },
174
210
  // For OME-Zarr:
175
211
  [FileType.IMAGE_OME_ZARR]: {
176
212
  zip: FileType.IMAGE_OME_ZARR_ZIP,
package/dist-tsc/constants.d.ts CHANGED
@@ -21,8 +21,13 @@ export declare const ViewType: {
21
21
  FEATURE_VALUE_HISTOGRAM: string;
22
22
  DOT_PLOT: string;
23
23
  FEATURE_BAR_PLOT: string;
24
+ VOLCANO_PLOT: string;
25
+ OBS_SET_COMPOSITION_BAR_PLOT: string;
26
+ FEATURE_SET_ENRICHMENT_BAR_PLOT: string;
24
27
  BIOMARKER_SELECT: string;
28
+ COMPARATIVE_HEADING: string;
25
29
  LINK_CONTROLLER: string;
30
+ NEUROGLANCER: string;
26
31
  DUAL_SCATTERPLOT: string;
27
32
  TREEMAP: string;
28
33
  };
@@ -41,6 +46,10 @@ export declare const DataType: {
41
46
  OBS_LOCATIONS: string;
42
47
  SAMPLE_SETS: string;
43
48
  SAMPLE_EDGES: string;
49
+ COMPARISON_METADATA: string;
50
+ FEATURE_STATS: string;
51
+ FEATURE_SET_STATS: string;
52
+ OBS_SET_STATS: string;
44
53
  };
45
54
  export declare const AsyncFunctionType: {
46
55
  AUTOCOMPLETE_FEATURE: string;
@@ -85,6 +94,10 @@ export declare const FileType: {
85
94
  FEATURE_LABELS_ANNDATA_ZARR: string;
86
95
  SAMPLE_EDGES_ANNDATA_ZARR: string;
87
96
  SAMPLE_SETS_ANNDATA_ZARR: string;
97
+ COMPARISON_METADATA_ANNDATA_ZARR: string;
98
+ COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR: string;
99
+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR: string;
100
+ COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR: string;
88
101
  OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: string;
89
102
  OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: string;
90
103
  OBS_SETS_ANNDATA_ZARR_ZIP: string;
@@ -97,6 +110,10 @@ export declare const FileType: {
97
110
  FEATURE_LABELS_ANNDATA_ZARR_ZIP: string;
98
111
  SAMPLE_EDGES_ANNDATA_ZARR_ZIP: string;
99
112
  SAMPLE_SETS_ANNDATA_ZARR_ZIP: string;
113
+ COMPARISON_METADATA_ANNDATA_ZARR_ZIP: string;
114
+ COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR_ZIP: string;
115
+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR_ZIP: string;
116
+ COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR_ZIP: string;
100
117
  OBS_FEATURE_MATRIX_ANNDATA_H5AD: string;
101
118
  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: string;
102
119
  OBS_SETS_ANNDATA_H5AD: string;
@@ -109,6 +126,10 @@ export declare const FileType: {
109
126
  FEATURE_LABELS_ANNDATA_H5AD: string;
110
127
  SAMPLE_EDGES_ANNDATA_H5AD: string;
111
128
  SAMPLE_SETS_ANNDATA_H5AD: string;
129
+ COMPARISON_METADATA_ANNDATA_H5AD: string;
130
+ COMPARATIVE_FEATURE_STATS_ANNDATA_H5AD: string;
131
+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_H5AD: string;
132
+ COMPARATIVE_OBS_SET_STATS_ANNDATA_H5AD: string;
112
133
  IMAGE_SPATIALDATA_ZARR: string;
113
134
  LABELS_SPATIALDATA_ZARR: string;
114
135
  SHAPES_SPATIALDATA_ZARR: string;
@@ -283,6 +304,10 @@ export declare const CoordinationType: {
283
304
  EMBEDDING_CONTOUR_PERCENTILES: string;
284
305
  CONTOUR_COLOR_ENCODING: string;
285
306
  CONTOUR_COLOR: string;
307
+ FEATURE_POINT_SIGNIFICANCE_THRESHOLD: string;
308
+ FEATURE_LABEL_SIGNIFICANCE_THRESHOLD: string;
309
+ FEATURE_POINT_FOLD_CHANGE_THRESHOLD: string;
310
+ FEATURE_LABEL_FOLD_CHANGE_THRESHOLD: string;
286
311
  HIERARCHY_LEVELS: string;
287
312
  };
288
313
  export declare const STATUS: {
@@ -314,6 +339,10 @@ export declare const ViewHelpMapping: {
314
339
  FEATURE_VALUE_HISTOGRAM: string;
315
340
  DOT_PLOT: string;
316
341
  FEATURE_BAR_PLOT: string;
342
+ NEUROGLANCER: string;
317
343
  TREEMAP: string;
344
+ VOLCANO_PLOT: string;
345
+ OBS_SET_COMPOSITION_BAR_PLOT: string;
346
+ FEATURE_SET_ENRICHMENT_BAR_PLOT: string;
318
347
  };
319
348
  //# sourceMappingURL=constants.d.ts.map
package/dist-tsc/constants.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;CAsBpB,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;CAepB,CAAC;AAEF,eAAO,MAAM,iBAAiB;;;;;;;;;;CAc7B,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA2HpB,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAsI5B,CAAC;AAEF,eAAO,MAAM,MAAM;;;;CAIlB,CAAC;AAEF,eAAO,MAAM,eAAe;;;CAG3B,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;CAiB3B,CAAC"}
1
+ {"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;CA2BpB,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;CAmBpB,CAAC;AAEF,eAAO,MAAM,iBAAiB;;;;;;;;;;CAc7B,CAAC;AAEF,eAAO,MAAM,QAAQ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA4IpB,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA2I5B,CAAC;AAEF,eAAO,MAAM,MAAM;;;;CAIlB,CAAC;AAEF,eAAO,MAAM,eAAe;;;CAG3B,CAAC;AAEF;;;GAGG;AACH,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;CAqB3B,CAAC"}
package/dist-tsc/constants.js CHANGED
@@ -21,8 +21,13 @@ export const ViewType = {
21
21
  FEATURE_VALUE_HISTOGRAM: 'featureValueHistogram',
22
22
  DOT_PLOT: 'dotPlot',
23
23
  FEATURE_BAR_PLOT: 'featureBarPlot',
24
+ VOLCANO_PLOT: 'volcanoPlot',
25
+ OBS_SET_COMPOSITION_BAR_PLOT: 'obsSetCompositionBarPlot',
26
+ FEATURE_SET_ENRICHMENT_BAR_PLOT: 'featureSetEnrichmentBarPlot',
24
27
  BIOMARKER_SELECT: 'biomarkerSelect',
28
+ COMPARATIVE_HEADING: 'comparativeHeading',
25
29
  LINK_CONTROLLER: 'linkController',
30
+ NEUROGLANCER: 'neuroglancer',
26
31
  DUAL_SCATTERPLOT: 'dualScatterplot',
27
32
  TREEMAP: 'treemap',
28
33
  };
@@ -41,6 +46,10 @@ export const DataType = {
41
46
  OBS_LOCATIONS: 'obsLocations',
42
47
  SAMPLE_SETS: 'sampleSets',
43
48
  SAMPLE_EDGES: 'sampleEdges',
49
+ COMPARISON_METADATA: 'comparisonMetadata',
50
+ FEATURE_STATS: 'featureStats',
51
+ FEATURE_SET_STATS: 'featureSetStats',
52
+ OBS_SET_STATS: 'obsSetStats',
44
53
  };
45
54
  export const AsyncFunctionType = {
46
55
  // String input (rather than Node input)
@@ -92,6 +101,10 @@ export const FileType = {
92
101
  FEATURE_LABELS_ANNDATA_ZARR: 'featureLabels.anndata.zarr',
93
102
  SAMPLE_EDGES_ANNDATA_ZARR: 'sampleEdges.anndata.zarr',
94
103
  SAMPLE_SETS_ANNDATA_ZARR: 'sampleSets.anndata.zarr',
104
+ COMPARISON_METADATA_ANNDATA_ZARR: 'comparisonMetadata.anndata.zarr',
105
+ COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR: 'comparativeFeatureStats.anndata.zarr',
106
+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR: 'comparativeFeatureSetStats.anndata.zarr',
107
+ COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR: 'comparativeObsSetStats.anndata.zarr',
95
108
  // AnnData - zipped
96
109
  OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: 'obsFeatureMatrix.anndata.zarr.zip',
97
110
  OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: 'obsFeatureColumns.anndata.zarr.zip',
@@ -105,6 +118,10 @@ export const FileType = {
105
118
  FEATURE_LABELS_ANNDATA_ZARR_ZIP: 'featureLabels.anndata.zarr.zip',
106
119
  SAMPLE_EDGES_ANNDATA_ZARR_ZIP: 'sampleEdges.anndata.zarr.zip',
107
120
  SAMPLE_SETS_ANNDATA_ZARR_ZIP: 'sampleSets.anndata.zarr.zip',
121
+ COMPARISON_METADATA_ANNDATA_ZARR_ZIP: 'comparisonMetadata.anndata.zarr.zip',
122
+ COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR_ZIP: 'comparativeFeatureStats.anndata.zarr.zip',
123
+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR_ZIP: 'comparativeFeatureSetStats.anndata.zarr.zip',
124
+ COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR_ZIP: 'comparativeObsSetStats.anndata.zarr.zip',
108
125
  // AnnData - h5ad via reference spec
109
126
  OBS_FEATURE_MATRIX_ANNDATA_H5AD: 'obsFeatureMatrix.anndata.h5ad',
110
127
  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: 'obsFeatureColumns.anndata.h5ad',
@@ -118,6 +135,10 @@ export const FileType = {
118
135
  FEATURE_LABELS_ANNDATA_H5AD: 'featureLabels.anndata.h5ad',
119
136
  SAMPLE_EDGES_ANNDATA_H5AD: 'sampleEdges.anndata.h5ad',
120
137
  SAMPLE_SETS_ANNDATA_H5AD: 'sampleSets.anndata.h5ad',
138
+ COMPARISON_METADATA_ANNDATA_H5AD: 'comparisonMetadata.anndata.h5ad',
139
+ COMPARATIVE_FEATURE_STATS_ANNDATA_H5AD: 'comparativeFeatureStats.anndata.h5ad',
140
+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_H5AD: 'comparativeFeatureSetStats.anndata.h5ad',
141
+ COMPARATIVE_OBS_SET_STATS_ANNDATA_H5AD: 'comparativeObsSetStats.anndata.h5ad',
121
142
  // SpatialData
122
143
  IMAGE_SPATIALDATA_ZARR: 'image.spatialdata.zarr',
123
144
  LABELS_SPATIALDATA_ZARR: 'labels.spatialdata.zarr',
@@ -315,6 +336,11 @@ export const CoordinationType = {
315
336
  EMBEDDING_CONTOUR_PERCENTILES: 'embeddingContourPercentiles',
316
337
  CONTOUR_COLOR_ENCODING: 'contourColorEncoding',
317
338
  CONTOUR_COLOR: 'contourColor',
339
+ // For volcano plot:
340
+ FEATURE_POINT_SIGNIFICANCE_THRESHOLD: 'featurePointSignificanceThreshold',
341
+ FEATURE_LABEL_SIGNIFICANCE_THRESHOLD: 'featureLabelSignificanceThreshold',
342
+ FEATURE_POINT_FOLD_CHANGE_THRESHOLD: 'featurePointFoldChangeThreshold',
343
+ FEATURE_LABEL_FOLD_CHANGE_THRESHOLD: 'featureLabelFoldChangeThreshold',
318
344
  // Treemap
319
345
  HIERARCHY_LEVELS: 'hierarchyLevels',
320
346
  };
@@ -347,5 +373,9 @@ export const ViewHelpMapping = {
347
373
  FEATURE_VALUE_HISTOGRAM: 'The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).',
348
374
  DOT_PLOT: 'The dot plot displays summary information about expression of the selected features (e.g., genes) for each selected observation set (e.g., cell type).',
349
375
  FEATURE_BAR_PLOT: 'The feature bar plot displays one bar per observation (e.g., cell) along the x-axis, where the value of a selected feature (e.g., gene) is encoded along the y-axis.',
376
+ NEUROGLANCER: 'The Neuroglancer view displays 3d meshes using Neuroglancer developed by Google.',
350
377
  TREEMAP: 'The treemap provides an overview of the current state of sample-level or cell-level selection and filtering.',
378
+ VOLCANO_PLOT: 'The volcano plot displays differential expression results. Each data point represents a feature (as opposed to an observation).',
379
+ OBS_SET_COMPOSITION_BAR_PLOT: 'The set composition bar plot displays the results of a compositional analysis conducted using the scCODA method (Büttner et al. 2021 Nature Communications).',
380
+ FEATURE_SET_ENRICHMENT_BAR_PLOT: 'The feature set enrichment bar plot displays the results of a hypergeometric test applied to the differential expression test results to identify enriched pathway gene sets.',
351
381
  };
package/dist-tsc/coordination.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"coordination.d.ts","sourceRoot":"","sources":["../src/coordination.ts"],"names":[],"mappings":"AASA,eAAO,MAAM,mCAAmC,UAc/C,CAAC;AAEF;;;;;;;KAOK;AACL,eAAO,MAAM,4BAA4B;;;CAyfxC,CAAC"}
1
+ {"version":3,"file":"coordination.d.ts","sourceRoot":"","sources":["../src/coordination.ts"],"names":[],"mappings":"AASA,eAAO,MAAM,mCAAmC,UAc/C,CAAC;AAEF;;;;;;;KAOK;AACL,eAAO,MAAM,4BAA4B;;;CA8jBxC,CAAC"}
package/dist-tsc/coordination.js CHANGED
@@ -30,6 +30,9 @@ export const AUTO_INDEPENDENT_COORDINATION_TYPES = [
30
30
  * Keys here are the component registry keys.
31
31
  */
32
32
  export const COMPONENT_COORDINATION_TYPES = {
33
+ [ViewType.NEUROGLANCER]: [
34
+ CoordinationType.DATASET,
35
+ ],
33
36
  [ViewType.SCATTERPLOT]: [
34
37
  CoordinationType.DATASET,
35
38
  CoordinationType.OBS_TYPE,
@@ -499,8 +502,64 @@ export const COMPONENT_COORDINATION_TYPES = {
499
502
  CoordinationType.OBS_COLOR_ENCODING,
500
503
  CoordinationType.ADDITIONAL_OBS_SETS,
501
504
  ],
505
+ [ViewType.VOLCANO_PLOT]: [
506
+ CoordinationType.DATASET,
507
+ CoordinationType.OBS_TYPE,
508
+ CoordinationType.FEATURE_TYPE,
509
+ CoordinationType.SAMPLE_TYPE,
510
+ // For selection of case-control sets of samples:
511
+ CoordinationType.SAMPLE_SET_SELECTION,
512
+ // For selection of one-vs-others sets of observations:
513
+ CoordinationType.OBS_SET_SELECTION,
514
+ // TODO: CoordinationType.FEATURE_SET_SELECTION,
515
+ // TODO: CoordinationType.FEATURE_SET_HIGHLIGHT,
516
+ // TODO: CoordinationType.FEATURE_SET_COLOR,
517
+ CoordinationType.FEATURE_HIGHLIGHT,
518
+ CoordinationType.FEATURE_SELECTION,
519
+ CoordinationType.FEATURE_VALUE_COLORMAP,
520
+ CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
521
+ // TODO: CoordinationType.FEATURE_COLOR_ENCODING,
522
+ // TODO: CoordinationType.ADDITIONAL_FEATURE_SETS,
523
+ CoordinationType.TOOLTIPS_VISIBLE,
524
+ CoordinationType.ADDITIONAL_OBS_SETS,
525
+ CoordinationType.OBS_SET_COLOR,
526
+ CoordinationType.SAMPLE_SET_COLOR,
527
+ CoordinationType.FEATURE_POINT_SIGNIFICANCE_THRESHOLD,
528
+ CoordinationType.FEATURE_LABEL_SIGNIFICANCE_THRESHOLD,
529
+ CoordinationType.FEATURE_POINT_FOLD_CHANGE_THRESHOLD,
530
+ CoordinationType.FEATURE_LABEL_FOLD_CHANGE_THRESHOLD,
531
+ ],
532
+ [ViewType.OBS_SET_COMPOSITION_BAR_PLOT]: [
533
+ CoordinationType.DATASET,
534
+ CoordinationType.OBS_TYPE,
535
+ CoordinationType.SAMPLE_TYPE,
536
+ // For selection of case-control sets of samples:
537
+ CoordinationType.SAMPLE_SET_SELECTION,
538
+ // For selection of one-vs-others sets of observations:
539
+ CoordinationType.OBS_SET_SELECTION,
540
+ CoordinationType.ADDITIONAL_OBS_SETS,
541
+ CoordinationType.OBS_SET_COLOR,
542
+ CoordinationType.SAMPLE_SET_COLOR,
543
+ ],
544
+ [ViewType.FEATURE_SET_ENRICHMENT_BAR_PLOT]: [
545
+ CoordinationType.DATASET,
546
+ CoordinationType.OBS_TYPE,
547
+ CoordinationType.FEATURE_TYPE,
548
+ CoordinationType.SAMPLE_TYPE,
549
+ // For selection of case-control sets of samples:
550
+ CoordinationType.SAMPLE_SET_SELECTION,
551
+ // For selection of one-vs-others sets of observations:
552
+ CoordinationType.OBS_SET_SELECTION,
553
+ CoordinationType.ADDITIONAL_OBS_SETS,
554
+ CoordinationType.OBS_SET_COLOR,
555
+ CoordinationType.SAMPLE_SET_COLOR,
556
+ CoordinationType.FEATURE_SELECTION,
557
+ ],
502
558
  [ViewType.LINK_CONTROLLER]: [],
503
559
  [ViewType.BIOMARKER_SELECT]: [
560
+ CoordinationType.DATASET,
561
+ CoordinationType.OBS_TYPE,
562
+ CoordinationType.SAMPLE_TYPE,
504
563
  CoordinationType.FEATURE_SELECTION,
505
564
  CoordinationType.SAMPLE_SET_SELECTION,
506
565
  CoordinationType.SAMPLE_SET_FILTER,
@@ -508,6 +567,16 @@ export const COMPONENT_COORDINATION_TYPES = {
508
567
  CoordinationType.OBS_SET_FILTER,
509
568
  // TODO: create coordination types for internal state of the biomarker selection view?
510
569
  ],
570
+ [ViewType.COMPARATIVE_HEADING]: [
571
+ CoordinationType.DATASET,
572
+ CoordinationType.OBS_TYPE,
573
+ CoordinationType.SAMPLE_TYPE,
574
+ CoordinationType.FEATURE_SELECTION,
575
+ CoordinationType.SAMPLE_SET_SELECTION,
576
+ CoordinationType.SAMPLE_SET_FILTER,
577
+ CoordinationType.OBS_SET_SELECTION,
578
+ CoordinationType.OBS_SET_FILTER,
579
+ ],
511
580
  [ViewType.TREEMAP]: [
512
581
  CoordinationType.DATASET,
513
582
  CoordinationType.OBS_TYPE,
package/dist-tsc/version.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "note": "This file is autogenerated by .changeset/post-changelog.mjs.",
3
- "version": "3.5.7",
4
- "date": "2025-02-19",
3
+ "version": "3.5.8",
4
+ "date": "2025-03-06",
5
5
  "branch": "changeset-release/main",
6
- "hash": "a4bc3a6a"
6
+ "hash": "9066c55a"
7
7
  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@vitessce/constants-internal",
3
- "version": "3.5.7",
3
+ "version": "3.5.8",
4
4
  "author": "HIDIVE Lab at HMS",
5
5
  "homepage": "http://vitessce.io",
6
6
  "repository": {
package/src/constant-relationships.ts CHANGED
@@ -32,6 +32,10 @@ export const FILE_TYPE_DATA_TYPE_MAPPING = {
32
32
  [FileType.FEATURE_LABELS_ANNDATA_ZARR]: DataType.FEATURE_LABELS,
33
33
  [FileType.SAMPLE_EDGES_ANNDATA_ZARR]: DataType.SAMPLE_EDGES,
34
34
  [FileType.SAMPLE_SETS_ANNDATA_ZARR]: DataType.SAMPLE_SETS,
35
+ [FileType.COMPARISON_METADATA_ANNDATA_ZARR]: DataType.COMPARISON_METADATA,
36
+ [FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR]: DataType.FEATURE_STATS,
37
+ [FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR]: DataType.FEATURE_SET_STATS,
38
+ [FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR]: DataType.OBS_SET_STATS,
35
39
  [FileType.IMAGE_OME_TIFF]: DataType.IMAGE,
36
40
  [FileType.OBS_SEGMENTATIONS_OME_TIFF]: DataType.OBS_SEGMENTATIONS,
37
41
  [FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
@@ -121,6 +125,22 @@ export const DATA_TYPE_COORDINATION_VALUE_USAGE = {
121
125
  CoordinationType.OBS_TYPE,
122
126
  CoordinationType.SAMPLE_TYPE,
123
127
  ],
128
+ [DataType.COMPARISON_METADATA]: [
129
+ CoordinationType.OBS_TYPE,
130
+ CoordinationType.SAMPLE_TYPE,
131
+ ],
132
+ [DataType.FEATURE_STATS]: [
133
+ CoordinationType.FEATURE_TYPE,
134
+ // TODO: should sampleType, obsSetSelection, and/or sampleSetSelection be used here?
135
+ ],
136
+ [DataType.FEATURE_SET_STATS]: [
137
+ CoordinationType.FEATURE_TYPE,
138
+ // TODO: should sampleType, obsSetSelection, and/or sampleSetSelection be used here?
139
+ ],
140
+ [DataType.OBS_SET_STATS]: [
141
+ CoordinationType.OBS_TYPE,
142
+ // TODO: should sampleType, obsSetSelection, and/or sampleSetSelection be used here?
143
+ ],
124
144
  };
125
145
 
126
146
  // For Zarr-based file types, we keep a mapping to file types
@@ -176,6 +196,23 @@ export const ALT_ZARR_STORE_TYPES = {
176
196
  zip: FileType.SAMPLE_SETS_ANNDATA_ZARR_ZIP,
177
197
  h5ad: FileType.SAMPLE_SETS_ANNDATA_H5AD,
178
198
  },
199
+ [FileType.COMPARISON_METADATA_ANNDATA_ZARR]: {
200
+ zip: FileType.COMPARISON_METADATA_ANNDATA_ZARR_ZIP,
201
+ h5ad: FileType.COMPARISON_METADATA_ANNDATA_H5AD,
202
+ },
203
+ [FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR]: {
204
+ zip: FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR_ZIP,
205
+ h5ad: FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_H5AD,
206
+ },
207
+ [FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR]: {
208
+ zip: FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR_ZIP,
209
+ h5ad: FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_H5AD,
210
+ },
211
+ [FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR]: {
212
+ zip: FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR_ZIP,
213
+ h5ad: FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_H5AD,
214
+ },
215
+
179
216
  // For OME-Zarr:
180
217
  [FileType.IMAGE_OME_ZARR]: {
181
218
  zip: FileType.IMAGE_OME_ZARR_ZIP,
package/src/constants.ts CHANGED
@@ -21,8 +21,13 @@ export const ViewType = {
21
21
  FEATURE_VALUE_HISTOGRAM: 'featureValueHistogram',
22
22
  DOT_PLOT: 'dotPlot',
23
23
  FEATURE_BAR_PLOT: 'featureBarPlot',
24
+ VOLCANO_PLOT: 'volcanoPlot',
25
+ OBS_SET_COMPOSITION_BAR_PLOT: 'obsSetCompositionBarPlot',
26
+ FEATURE_SET_ENRICHMENT_BAR_PLOT: 'featureSetEnrichmentBarPlot',
24
27
  BIOMARKER_SELECT: 'biomarkerSelect',
28
+ COMPARATIVE_HEADING: 'comparativeHeading',
25
29
  LINK_CONTROLLER: 'linkController',
30
+ NEUROGLANCER: 'neuroglancer',
26
31
  DUAL_SCATTERPLOT: 'dualScatterplot',
27
32
  TREEMAP: 'treemap',
28
33
  };
@@ -42,6 +47,10 @@ export const DataType = {
42
47
  OBS_LOCATIONS: 'obsLocations',
43
48
  SAMPLE_SETS: 'sampleSets',
44
49
  SAMPLE_EDGES: 'sampleEdges',
50
+ COMPARISON_METADATA: 'comparisonMetadata',
51
+ FEATURE_STATS: 'featureStats',
52
+ FEATURE_SET_STATS: 'featureSetStats',
53
+ OBS_SET_STATS: 'obsSetStats',
45
54
  };
46
55
 
47
56
  export const AsyncFunctionType = {
@@ -97,6 +106,12 @@ export const FileType = {
97
106
  FEATURE_LABELS_ANNDATA_ZARR: 'featureLabels.anndata.zarr',
98
107
  SAMPLE_EDGES_ANNDATA_ZARR: 'sampleEdges.anndata.zarr',
99
108
  SAMPLE_SETS_ANNDATA_ZARR: 'sampleSets.anndata.zarr',
109
+
110
+ COMPARISON_METADATA_ANNDATA_ZARR: 'comparisonMetadata.anndata.zarr',
111
+ COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR: 'comparativeFeatureStats.anndata.zarr',
112
+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR: 'comparativeFeatureSetStats.anndata.zarr',
113
+ COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR: 'comparativeObsSetStats.anndata.zarr',
114
+
100
115
  // AnnData - zipped
101
116
  OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: 'obsFeatureMatrix.anndata.zarr.zip',
102
117
  OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: 'obsFeatureColumns.anndata.zarr.zip',
@@ -110,6 +125,12 @@ export const FileType = {
110
125
  FEATURE_LABELS_ANNDATA_ZARR_ZIP: 'featureLabels.anndata.zarr.zip',
111
126
  SAMPLE_EDGES_ANNDATA_ZARR_ZIP: 'sampleEdges.anndata.zarr.zip',
112
127
  SAMPLE_SETS_ANNDATA_ZARR_ZIP: 'sampleSets.anndata.zarr.zip',
128
+
129
+ COMPARISON_METADATA_ANNDATA_ZARR_ZIP: 'comparisonMetadata.anndata.zarr.zip',
130
+ COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR_ZIP: 'comparativeFeatureStats.anndata.zarr.zip',
131
+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR_ZIP: 'comparativeFeatureSetStats.anndata.zarr.zip',
132
+ COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR_ZIP: 'comparativeObsSetStats.anndata.zarr.zip',
133
+
113
134
  // AnnData - h5ad via reference spec
114
135
  OBS_FEATURE_MATRIX_ANNDATA_H5AD: 'obsFeatureMatrix.anndata.h5ad',
115
136
  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: 'obsFeatureColumns.anndata.h5ad',
@@ -123,6 +144,11 @@ export const FileType = {
123
144
  FEATURE_LABELS_ANNDATA_H5AD: 'featureLabels.anndata.h5ad',
124
145
  SAMPLE_EDGES_ANNDATA_H5AD: 'sampleEdges.anndata.h5ad',
125
146
  SAMPLE_SETS_ANNDATA_H5AD: 'sampleSets.anndata.h5ad',
147
+
148
+ COMPARISON_METADATA_ANNDATA_H5AD: 'comparisonMetadata.anndata.h5ad',
149
+ COMPARATIVE_FEATURE_STATS_ANNDATA_H5AD: 'comparativeFeatureStats.anndata.h5ad',
150
+ COMPARATIVE_FEATURE_SET_STATS_ANNDATA_H5AD: 'comparativeFeatureSetStats.anndata.h5ad',
151
+ COMPARATIVE_OBS_SET_STATS_ANNDATA_H5AD: 'comparativeObsSetStats.anndata.h5ad',
126
152
  // SpatialData
127
153
  IMAGE_SPATIALDATA_ZARR: 'image.spatialdata.zarr',
128
154
  LABELS_SPATIALDATA_ZARR: 'labels.spatialdata.zarr',
@@ -321,6 +347,11 @@ export const CoordinationType = {
321
347
  EMBEDDING_CONTOUR_PERCENTILES: 'embeddingContourPercentiles',
322
348
  CONTOUR_COLOR_ENCODING: 'contourColorEncoding',
323
349
  CONTOUR_COLOR: 'contourColor',
350
+ // For volcano plot:
351
+ FEATURE_POINT_SIGNIFICANCE_THRESHOLD: 'featurePointSignificanceThreshold',
352
+ FEATURE_LABEL_SIGNIFICANCE_THRESHOLD: 'featureLabelSignificanceThreshold',
353
+ FEATURE_POINT_FOLD_CHANGE_THRESHOLD: 'featurePointFoldChangeThreshold',
354
+ FEATURE_LABEL_FOLD_CHANGE_THRESHOLD: 'featureLabelFoldChangeThreshold',
324
355
  // Treemap
325
356
  HIERARCHY_LEVELS: 'hierarchyLevels',
326
357
  };
@@ -356,5 +387,9 @@ export const ViewHelpMapping = {
356
387
  FEATURE_VALUE_HISTOGRAM: 'The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).',
357
388
  DOT_PLOT: 'The dot plot displays summary information about expression of the selected features (e.g., genes) for each selected observation set (e.g., cell type).',
358
389
  FEATURE_BAR_PLOT: 'The feature bar plot displays one bar per observation (e.g., cell) along the x-axis, where the value of a selected feature (e.g., gene) is encoded along the y-axis.',
390
+ NEUROGLANCER: 'The Neuroglancer view displays 3d meshes using Neuroglancer developed by Google.',
359
391
  TREEMAP: 'The treemap provides an overview of the current state of sample-level or cell-level selection and filtering.',
392
+ VOLCANO_PLOT: 'The volcano plot displays differential expression results. Each data point represents a feature (as opposed to an observation).',
393
+ OBS_SET_COMPOSITION_BAR_PLOT: 'The set composition bar plot displays the results of a compositional analysis conducted using the scCODA method (Büttner et al. 2021 Nature Communications).',
394
+ FEATURE_SET_ENRICHMENT_BAR_PLOT: 'The feature set enrichment bar plot displays the results of a hypergeometric test applied to the differential expression test results to identify enriched pathway gene sets.',
360
395
  };
package/src/coordination.ts CHANGED
@@ -32,6 +32,9 @@ export const AUTO_INDEPENDENT_COORDINATION_TYPES = [
32
32
  * Keys here are the component registry keys.
33
33
  */
34
34
  export const COMPONENT_COORDINATION_TYPES = {
35
+ [ViewType.NEUROGLANCER]: [
36
+ CoordinationType.DATASET,
37
+ ],
35
38
  [ViewType.SCATTERPLOT]: [
36
39
  CoordinationType.DATASET,
37
40
  CoordinationType.OBS_TYPE,
@@ -501,8 +504,64 @@ export const COMPONENT_COORDINATION_TYPES = {
501
504
  CoordinationType.OBS_COLOR_ENCODING,
502
505
  CoordinationType.ADDITIONAL_OBS_SETS,
503
506
  ],
507
+ [ViewType.VOLCANO_PLOT]: [
508
+ CoordinationType.DATASET,
509
+ CoordinationType.OBS_TYPE,
510
+ CoordinationType.FEATURE_TYPE,
511
+ CoordinationType.SAMPLE_TYPE,
512
+ // For selection of case-control sets of samples:
513
+ CoordinationType.SAMPLE_SET_SELECTION,
514
+ // For selection of one-vs-others sets of observations:
515
+ CoordinationType.OBS_SET_SELECTION,
516
+ // TODO: CoordinationType.FEATURE_SET_SELECTION,
517
+ // TODO: CoordinationType.FEATURE_SET_HIGHLIGHT,
518
+ // TODO: CoordinationType.FEATURE_SET_COLOR,
519
+ CoordinationType.FEATURE_HIGHLIGHT,
520
+ CoordinationType.FEATURE_SELECTION,
521
+ CoordinationType.FEATURE_VALUE_COLORMAP,
522
+ CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
523
+ // TODO: CoordinationType.FEATURE_COLOR_ENCODING,
524
+ // TODO: CoordinationType.ADDITIONAL_FEATURE_SETS,
525
+ CoordinationType.TOOLTIPS_VISIBLE,
526
+ CoordinationType.ADDITIONAL_OBS_SETS,
527
+ CoordinationType.OBS_SET_COLOR,
528
+ CoordinationType.SAMPLE_SET_COLOR,
529
+ CoordinationType.FEATURE_POINT_SIGNIFICANCE_THRESHOLD,
530
+ CoordinationType.FEATURE_LABEL_SIGNIFICANCE_THRESHOLD,
531
+ CoordinationType.FEATURE_POINT_FOLD_CHANGE_THRESHOLD,
532
+ CoordinationType.FEATURE_LABEL_FOLD_CHANGE_THRESHOLD,
533
+ ],
534
+ [ViewType.OBS_SET_COMPOSITION_BAR_PLOT]: [
535
+ CoordinationType.DATASET,
536
+ CoordinationType.OBS_TYPE,
537
+ CoordinationType.SAMPLE_TYPE,
538
+ // For selection of case-control sets of samples:
539
+ CoordinationType.SAMPLE_SET_SELECTION,
540
+ // For selection of one-vs-others sets of observations:
541
+ CoordinationType.OBS_SET_SELECTION,
542
+ CoordinationType.ADDITIONAL_OBS_SETS,
543
+ CoordinationType.OBS_SET_COLOR,
544
+ CoordinationType.SAMPLE_SET_COLOR,
545
+ ],
546
+ [ViewType.FEATURE_SET_ENRICHMENT_BAR_PLOT]: [
547
+ CoordinationType.DATASET,
548
+ CoordinationType.OBS_TYPE,
549
+ CoordinationType.FEATURE_TYPE,
550
+ CoordinationType.SAMPLE_TYPE,
551
+ // For selection of case-control sets of samples:
552
+ CoordinationType.SAMPLE_SET_SELECTION,
553
+ // For selection of one-vs-others sets of observations:
554
+ CoordinationType.OBS_SET_SELECTION,
555
+ CoordinationType.ADDITIONAL_OBS_SETS,
556
+ CoordinationType.OBS_SET_COLOR,
557
+ CoordinationType.SAMPLE_SET_COLOR,
558
+ CoordinationType.FEATURE_SELECTION,
559
+ ],
504
560
  [ViewType.LINK_CONTROLLER]: [],
505
561
  [ViewType.BIOMARKER_SELECT]: [
562
+ CoordinationType.DATASET,
563
+ CoordinationType.OBS_TYPE,
564
+ CoordinationType.SAMPLE_TYPE,
506
565
  CoordinationType.FEATURE_SELECTION,
507
566
  CoordinationType.SAMPLE_SET_SELECTION,
508
567
  CoordinationType.SAMPLE_SET_FILTER,
@@ -510,6 +569,16 @@ export const COMPONENT_COORDINATION_TYPES = {
510
569
  CoordinationType.OBS_SET_FILTER,
511
570
  // TODO: create coordination types for internal state of the biomarker selection view?
512
571
  ],
572
+ [ViewType.COMPARATIVE_HEADING]: [
573
+ CoordinationType.DATASET,
574
+ CoordinationType.OBS_TYPE,
575
+ CoordinationType.SAMPLE_TYPE,
576
+ CoordinationType.FEATURE_SELECTION,
577
+ CoordinationType.SAMPLE_SET_SELECTION,
578
+ CoordinationType.SAMPLE_SET_FILTER,
579
+ CoordinationType.OBS_SET_SELECTION,
580
+ CoordinationType.OBS_SET_FILTER,
581
+ ],
513
582
  [ViewType.TREEMAP]: [
514
583
  CoordinationType.DATASET,
515
584
  CoordinationType.OBS_TYPE,
package/src/version.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "note": "This file is autogenerated by .changeset/post-changelog.mjs.",
3
- "version": "3.5.7",
4
- "date": "2025-02-19",
3
+ "version": "3.5.8",
4
+ "date": "2025-03-06",
5
5
  "branch": "changeset-release/main",
6
- "hash": "a4bc3a6a"
6
+ "hash": "9066c55a"
7
7
  }