When there is not per-observation centroids, fall back to using the mouse position for tooltips in the spatial view. (@vitessce/spatial) (#1458)
Fix duplicate URLs appearing in download dropdown by filtering based on names. (@vitessce/vit-s) (#1458)
Added functions to the VitessceConfig object-oriented configuration APIs to support multi-level and meta (i.e., complex) coordination. (@vitessce/config) (#1561)
Implement hints for zero config mode. (@vitessce/config, docs) (#1597)
- Added a list of hints that user will select from, when using the zero config mode feature.
- Modified the user interface, defined in _ViewConfigEditor.js:
  - Defined a list of hints, which depend on the types of the files the user pastes URLs for.
  - Removed the Generate Config button. Now each hint is a button that generates the view config when pressed.
- Created a new file constants.js in packages/config that defines the range of supported hints, along with the name and coordinates of the desired layers.
- Modified VitessceAutoConfig.js:
  - Added a function to return the type of files the user pasted the URLs for. The function is used in _ViewConfigEditor.js to determine what set of hints to display.
  - Adapted the existing code to take selected hint into an account, when creating the view config.
Update styling of UI for auto-config layout hints in App page of docs. (docs) (#1597)
Make example packages private to prevent changesets from publishing to NPM (@vitessce/example-configs, @vitessce/example-plugins) (#1496)

3.0.1

Diff

keller-mark

published 3.0.1 • 2 years ago

Changelog

Source

3.0.1 - 2023-06-30

Added

Add a URL param option to the demo site to wrap <Vitessce/> in <React.StrictMode/>
Added a dropdown in FeatureList that allows the user to:
- select between alphabetical and original ordering for the feature list.
- show two columns in the feature list if the feature has a second identifier associated.
Add initial config logging in <Vitessce/> for the pre-upgrade view config.
Added support for generating view-config for Anndata-Zarr files that don't have .zmetadata file in the folder.
Turn on unit test coverage in Vitest config.
Add useInitialCoordination hook to get the values of the coordination space from the initial config, which can be used for viewState reset buttons.
Use config object reference as hook dependency when no config.uid is present (to support both controlled and un-controlled component cases).
Initialize Zustand store using closure over createViewConfigStore function, rather than via useEffect.
Implement basic solution for multi ome-zarr images via image.raster.json

Changed

Fix Material UI import statement.
Implemented the functionality required to re-order the feature list, based on the selection from the dropdown:
- added state variables featureListSort and showFeatureTable.
- hooked the state variables to FeatureListOptions and to FeatureList.
Fix Heatmap bug causing incorrect positioning of tooltip when using featureLabels mapping.
Modified the AnndataZarrAutoConfig class:
- added a parser function that generates metadata summary without reading .zmetadata file.
- the class calls the parser function if no .zmetadata file is present in the given URL.
Implement custom createGenerateClassName without random numbers involved to ensure deterministic class names.
- Rename makeStyles keys to be more specific to avoid conflicts.
Only generate ESM builds for vitessce and @vitessce/dev.
Use @tanstack/react-query for data fetching.
Fixed a bug in SetManager popover menu, where the text is not visible in vitessce.io in dark mode.

3.0.0

Diff

keller-mark

published 3.0.0 • 2 years ago

Changelog

Source

3.0.0 - 2023-05-24

Added

Added a legend for quantitative color scales in the SpatialSubscriber and EmbeddingScatterplotSubscriber views.
Support for automatic view config generation for OME-TIFF, Anndata-Zarr and OME-ZARR file formats.
Added a speaker icon to the documentation nav bar for using the International Phonetic Alphabet (IPA) notation to demonstrate how to pronounce Vitessce.
Added image.ome-tiff and obsSegmentations.ome-tiff file types.
Added coordinateTransformation file type options for image.ome-tiff and image.ome-zarr.
Modified the styling of the Vega-lite tooltips, so that it matches the scatterplot/spatial/heatmap tooltips.
Fixed a small bug with the path configuration for the obsSets component when using zero config mode.
Add notes about branch naming conventions and pull request merge process to README
Added bidirectional interactions for the CellSetSizesPlot vega-lite plot to allow the Vitessce view to update and show the selected cluster on bar click.
Implemented a "select-only" option for the CellSetSizesPlot on shift+click.
Implemented ability to select a gene by clicking on the heatmap rows for a given gene.
Added developer troubleshooting instructions to README.
Add useFullResolutionImage to Spatial to allow for loading only full resolution image from pyramid.
Implemented ability to select an area on the Expression Histogram. On select, a new obs set selection is created. The new selection contains the ids of all obs that belong to the selected bars.
Add integration test for consumer site built with NextJS.
Implemented ability to show two columns in the feature-list view when each feature has a second identifer associated.
Add CITATION.cff
Added a button to recenter and rescale data to default for Scatterplot and Spatial views.
Removed the Select Rectangle button from Scatterplot and Spatial views.
Added option to disable tooltips on Heatmap and Scatterplot components. The option is available from the options control dropdown.
Added an option to skip sorting features alphabetically in feature list.
Add GitHub Action workflow to report bundle size in PRs.

Changed

Fix hot module reloading by refactoring JS files that export React components (the component needs to be the only export for HMR to work). Add react-refresh eslint plugin to check for this moving forward.
Fixes Go to Definition support in vscode (see https://github.com/microsoft/TypeScript/issues/49003#issuecomment-1164659854).
Refactor obsFeatureMatrix normalization logic out of data loader classes and into custom hooks that can be used in view implementations as-needed.
Fixed syntax highlighting for code examples and editor in documentation.
Added a new file VitessceAutoConfig.js with methods and classes that can generate view config, given a list of dataset URLs.
Added a new documentation page: default-config.md that describes the auto config generation functionality and how to use it.
Small changes to the layout of _ViewConfigEditor.js to accomodate the new functionality: added a space for pasting links and a "Generate Config" button.
Update Vitest configuration to only include test files contained within src directories.
Added signals tracking and handling in the vega-lite schema for CellSetSizesPlot component.
Modified the treeToSetSizesBySetNames function to return the setNamePath, so we can track which hierarchy the cluster represented by the clicked bar belongs to.
Modified the CellSetSizesPlotSubscriber component to reset cellSetSelection to equal setNamePath when user clicks on a bar in the CellSetSizesPlot component.
Changed VegaPlot.js to accept prop called setName and overwrite the default tooltip style of vega-tooltip.
Added a new styles.js file that defines the style of the vega-tooltips.
Changed CellSetSizesPlot.js and CellSetExpressionPlot.js to pass in setName as props when calling VegaPlot.
Added more complex logic in CellSetSizesPlotSubscriber.js to determine which bars should be displayed in CellSetSizesPlot.js.
Added a new set-path-utils file with the functions containing the more complex logic around choosing which hierarchy to display on the CellSetSizesPlot.
Added one more prop under data in CellSetSizesPlot, called isGrayedOut and made vega-lite to color in gray bars where this property is set to true.
Added obsSetExpansion to coordination scope and started using it in CellSetSizesPlotSubscriber.js.
Added handling for the onClick function in the Heatmap component. The Heatmap component calls the onHeatmapClick function, defined in the HeatmapSubscriber, every time a user clicks on the heatmap. The onHeatmapClick function sets the currently selected gene to be equal to the gene the user clicked at. It also sets the cell color encoding to geneSelection.
Upgrade Viv to 0.13.7
Fix physical size scaling for non-square 2D pixels.
Removes logic for tsconfig.json from the meta-updater script
Update issue template.
Update documentation: fix broken links to source code, move Showcase to its own page from About page, replace Roadmap page with link to GitHub project.
Updated how TypedArrays are diff-ed in BitmaskLayer to reduce memory usage.
Changed the ExpressionHistogramSubscriber component:
- Added ADDITIONAL_OBS_SETS, OBS_SET_COLOR, OBS_COLOR_ENCODING and OBS_SET_SELECTION coordination types to the Feature Histogram.
- Added a new function called onSelect, passed as props to ExpressionHistogram. On selection on ExpressionHistogram, the function computes what cell ids belong to that selection. Then calls the pre-existing setObsSelection function to create a new cell set with the cell ids.
Added a signal to ExpressionHistogram component, which calls onSelect, after 1 minute of debounce.
Replace Ajv with Zod.
- Add generic config schema.
- Add builder function for generating plugin-specific config schema.
- Reimplement config version upgrades.
Provide plugins as React props rather than registering them globally on window.
Use hooks in ObsSetsManagerSubscriber to improve controlled-component performance.
Revert change that removed airbnb eslint config.
Only set additionalObsSets in coordination space when upgrade was necessary to prevent infinite loop.
Fix bug causing cell set hierarchy created via Create hierarchy button to contain the string undefined (e.g., My hierarchy 1undefined)
Fix bug in CellSetSizesPlotSubscriber causing page to crash when no obsSets view is present (due to expectation of initialized obsSetSelection and obsSetExpansion coordination values).
Fix bug causing incorrect gene selection upon heatmap click when featureLabels are used (such as in the case of gene aliases used in the HuBMAP data portal view configs).
Added a new prop to FeatureListSubscriber to read in showTable, having it false by default.
Modified the FeatureList component to pass in 2 columns and 2 column labels if showTable is true, otherwise just 1 column and 1 columnLabel if showTable is false.
Modified the SelectableTable component and the table styles to handle showing 2 cells per row.
Use es2019 in Vite bundle targets for packages/main/prod and packages/main/dev to support HuBMAP portal-ui.
Changes in ToolMenu:
- Added a new button that calls onRecenterButtonCLick function on click.
- Added css for the new button and introduced differentiation between a button and a tool.
Added a new function recenter to AbstractSpatialOrScatterplot that gets overriden by descendants.
- Added an implementation of that function in Spatial and Scatterplot.
- The function is passed to ToolMenu as prop by AbstractSpatialOrScatterplot and called on click.
Removed the select rectangle tool and all references to it.
Added a state variable called originalViewState in SpatialSubscriber and EmbeddingScatterplotSubscriber.
- originalViewState holds the value of the initial position of the view and is used for recentering.
Fix bug preventing correct view sizing upon config prop change when <Vitessce/> used as a controlled component.
Modified HeatmapOptions, SpatialOptions and ScatterplotOptions components - added a checkbox for making the tooltip not visible.
Added a tooltipsVisible to the coordination scope for Heatmap, Spatial and Scatterplot coordination types. Its default value is true. Modified the components to hide the tooltip if tooltipVsisible is false.
Removed disableTooltip from props.
Fix bug that may cause originalViewState.target to not be an array as expected.
Adjust the code in onHover in Heatmap.js to track cell position also for cells that are on the cell set bar.
Add function useGetObsMembership in hooks.js to get the full path of the cell that was clicked.
Adjusted the onHeatmapClick function in HeatmapSubscriber.js to distinguish between clicks on the heatmap and clicks on the cell set bar and take according actions.
Added a prop sort in FeatureListSubscriber, with default value equal to alphabetical.
Modified component FeatureList so that if sort is not equal to alphabetical, then sorting of data is skipped and the order of feature listis the same as original.
Fixed equality check when creating default model matrices for sizes
Split useEffect into useMemo + useEffect in SpatialSubscriber to fix infinite loop for neumann-2020 demo on the docs site.
Delay computing the initial view state longer in EmbeddingScatterplotSubscriber to ensure the view width/height is finished animating.
Made the cursor type to pointer when the user is hovering over the heatmap.
Fixed a bug in CellSetSizesPlotSubscriber plot causing rending of empty CellSetSizesPlot when there is no obsSets view (due to expectation of initialised cellSetExpanded coordination value).
Created FeatureListOptions component, which allows the user to change the sorting order of the feature list.

2.0.3

Diff

keller-mark

published 2.0.3 • 2 years ago

Changelog

Source

2.0.3 - 2023-02-01

Added

Re-implemented PR 1240 (coordinationScopesBy)
Added MuData file types.
Added a uid prop for VitS to fix Jupyter notebook style conflicts caused by multiple Vitessce widget instances loaded in the same JupyterLab session.
Added !important statements to override Jupyter Notebook (classic) style conflicts.
Added vite.config.js and pnpm run bundle for bundling sub-packages as proper ESM.
Added test for a "consumer" package of the Vitessce sub-packages in consumer/ directory, with a corresponding cypress test in sites/html/cypress/e2e/html.spec.cy.js.

Changed

Converted all rem units to px to fix R/Python widget CSS bugs caused by different root style conflicts.
Comment out _DiffViewConfigSchema in the docs to fix bug.
Switched to using react via esm.sh rather than es-react via unpkg for the Cypress tests in sites/html.
Simplify HiGlass dynamic import (possible now since no longer using Webpack) to resolve bug in Vitessce Python.
Upgrade Viv to 0.13.6 to support OME-NGFF v0.4
Use pnpm pack in all subpackages so that outdated packages from NPM are not used during the consumer package install test.
Update GitHub Pages tutorial in docs.

2.0.3-beta.0

Diff

keller-mark

published 2.0.3-beta.0 • 2 years ago

2.0.2

Diff

keller-mark

published 2.0.2 • 2 years ago

Changelog

Source

2.0.2 - 2022-12-09

Added

Added ./copy-dev.sh and ./copy-docs.sh instructions.
Added plugin registration exports to the main/all package exports, so that they are included in vitessce and @vitessce/dev package exports.

Changed

Don't await AnnData payloads that might be accessed in quickly repeatedly (i.e cache the promise, not the payload).
Fixed CSS bug in the development demo: changed overflow: hidden to overflow: scroll on the list of demos.
Bumped @vitejs/plugin-react version from 1.3.2 to 3.0.0-beta.0
Update parameters of MUI createGenerateClassName so that class names are deterministic
Fixed broken cell highlight crosshairs upon hover events in scatterplots/spatial/heatmap views by porting SCSS to MUI JSS.
Upgrade Viv to 0.13 and deck.gl to 8.8
Interleaved rgb images obey visibility prop
Added workaround in Spatial view for apparent bug in DeckGL PolygonLayer preventing passing polygon vertices via Uint32Array.

2.0.1

Diff

keller-mark

published 2.0.1 • 2 years ago

Changelog

Source

2.0.1 - 2022-11-20

Added

Added gating component that allows users to dynamically generate a scatterplot based on gene expression values.
- New coordination types of gatingFeatureSelectionX and gatingFeatureSelectionY for the values selected for the gating plot.
Added new arcsinh option for the coordinaition type featureValueTransform
Added new coordination type featureValueTransformCoefficient to apply a coefficent to a feature value transform.
Added new demos to the documentation to showcase the new obs-by-feature features.
Added ViewType as a main export from src/index.js alongside Component. Replaced Component with ViewType in the documentation.

Changed

Added new file type and data type constants.
Implemented "minimal" file types and data types:
- Added loaders for obsSets.json and obsSets.cell-sets.json.
- Added loaders for obsFeatureMatrix.clusters.json
- Added loaders for obsFeatureMatrix.genes.json
- Added loaders for obsLabels.cells.json, obsEmbedding.cells.json, obsLocations.cells.json, obsSegmentations.cells.json
- Added loaders for image.raster.json,obsSegmentations.raster.json, image.ome-zarr
- Added loaders for obsLabels.anndata-expression-matrix.zarr, featureLabels.anndata-expression-matrix.zarr, obsFeatureMatrix.anndata-expression-matrix.zarr
- Added loaders for obsFeatureMatrix.expression-matrix.zarr
- Added loaders for obsLabels.molecules.json and obsLocations.molecules.json
Added support for datatype: 'obs' in obsSets.schema.json
Added the property coordinationValues for view config file definitions.
Added the useMatchingLoader hook.
Added tests for checking that FileType constants have been mapped to corresponding data types and loader classes.
Implemented support for obsLabelsType which supersedes factors.
Implemented obs set membership tooltips.
Fixed bug in the v1.0.0 to v1.0.1 view config upgrade function caused by modification of a reference to the config object.
Changed the VitessceConfig constructor and VitessceConfigDataset.addFile method to use named arguments via JS objects.
Renamed and moved components
- genes/Genes -> feature-list/FeatureList
- sets/CellSetsManagerSubscriber -> obs-sets/ObsSetsManagerSubscriber
- sets/CellSetExpressionPlot -> statistical-plots/CellSetExpressionPlot
- sets/CellSetSizesPlot -> statistical-plots/CellSetSizesPlot
- genes/ExpressionHistogram -> statistical-plots/ExpressionHistogram
Monorepo
- Change <Vitessce/> -> <VitS/> within @vitessce/vit-s
- Wrote blog post
- Updated docs to make them compatible with new build setup
- Converted SCSS to JSS, for both external and internal stylesheets
- Converted unit/component testing setup to jest/vitest/react-testing-library
- Converted demo development server to vite
- Converted inline worker bundling to @vitessce/workers sub-package with rollup + rollup plugin
- Converted SVG React component imports to @vitessce/icons sub-package with vite + svgr
- Converted glslify #pragma + webpack plugin to glslify CLI in @vitessce/gl/src/glsl with string manipulation to prevent need for plugin
Make sure to exclude the background image when using transparentColor
Fixed bug preventing onConfigChange from being called upon view resize events.