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CHANGELOG.md

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0.6.0 - in progress

  • Changed the overall layout of the tool to be more visually organized and less complex
  • Removed a search bar in the higlass track, and add it in a title bar of the Cistrome Explorer.
  • Added a 'Show Instructions' button to show the hidden control buttons entirely and provide detailed textual instructions w/ tooltips upon mouse hover
  • Supported aggregating rows by tissue type
  • Showed aggregated bar charts for all samples
  • Allowed adding a bar track for selected row
  • Added a scale track (arrow) on the top that shows the length of current view window

0.5.0

Added

  • Undo/Redu interactions added in Cistrome Explorer.
  • Added an onOptions API in HiGlassMeta to change the wrapper options outside the library.
  • Added a menu panel that shows examples datasets and any other high-level options for HiGlassMeta.
  • Added linking tracks with background color upon mouse hover.
  • Added resolveYScale and sort options for using track-specific Y-axis scale.
  • Added line/band connections between tracks whey they use different y-axis scales.
  • Added width options that set the initial size of vertical tracks along x-axis.
  • Added an onRemoveAllSort API in HiGlassMeta for removing all sort options outside of the library.

Changed

  • Moved CistromeToolkit to the sibling of CistromeHGW.
  • Rename HiGlassWithMeta to HiGlassMeta.
  • Upgraded to HiGlass version 1.10.2
  • Fix the bug on highlighting rows in dendrograms.
  • Hide track titles upon mouse hover for addressing visual overlap.
  • Changed the row highlighting method, from reverse highlighting to regular highlighting, i.e., highlight the selected rows.
  • Renamed subtree to ancestors for clarity.

0.4.0

Added

  • Added row aggregation options (e.g., rowAggregate) to aggregate rows based on nominal fields metadata.
  • Added visual indicators (vertical black bars) to show which rows are aggregated.

Changed

  • Changed the table view to be shown as a modal view.
  • Updated format of API results (e.g., use consistent letter cases and use scientific notations for long numbers).
  • Filtering information in range sliders and keyword search boxes is based on the aggregated values (aggregatedRowInfo), instead of original rowInfo.
  • Fixed a SVG export bug which caused visualizations to be exported from previous datasets (corresponding to previous options prop values in the demo).
  • Updaetd a Cistrome DB Toolkit view to show two APIs with the history of request and data tables of each request.
  • Fixed z-index between track resizer, filtering box, and toolkit.
  • Rename the keyword search box (TrackRowSearch => TrackRowFilter).

0.3.0 - 05/27/20

Added

  • Added real data (quality score for each sample) for quantitative bar charts.
  • Added a mover component that allows one to interactively reposition the keyword search box.
  • Added filter reset buttons on the wrapper tracks to make it more accessible.
  • Added range condition in filter and highlighting options to enable filtering rows by value ranges.
  • Added a range slider to interactively filter rows by determining min and max cutoff values in quantitative bar charts, including stacked bar charts.
  • Added a vertical mouse wheel zooming feature for horizontal multivec tracks, activated when the Y key is pressed on the keyboard.
  • Added a minimum similarity bar in dendrogram to enable filtering rows by similarity scores.
  • Added a simple nav bar with links to GitHub and documentations.

Changed

  • Make keyword search box semi-transparent when blurred.
  • Changed the color of filter and sort icons when they are applied on a track as a visual indicator.
  • Changed the filtering interface for nominal values to use checkboxes.
  • Render range sliders and checkboxes for filtering interactions based on the original data.
  • Replace contains filtering condition to notOneOf.
  • Rename the filtering condition for tree type data from contains to subtree.
  • Reset buttons remove all filters related only to a certain field.
  • Each field has only one filterInfo for the simplicity.
  • Update dendrogram to visually encode similarity distance between nodes.

0.2.0 - 03/18/20

Added

  • Added a feature to interactively resize the width of each vertical track by dragging resizers.
  • Added a feature to interactively filter rows by keywords and reset all filters.
  • Added an option to specify multiple data fields in a single vertical track and implemented stacked bar charts for this case.
  • Added a feature to interactively filter rows by selecting a node in the dendrogram visualization.
  • Added x-axis ticks for quantitative bar plot visualizations for row info metadata.
  • Added transparent white background for visualization title text so that it does not visually interfere with the text for plot data labels.
  • Added measureText() two function for computing width and height of TwoText objects without rendering.
  • Added a search suggestion autocomplete feature.
  • Added a feature to request for bind TFs in a certain interval using Cistrome DB API and render the result in a simple data table.
  • Added a context menu for filtering or highlighting rows based on a nomival value in categorical bar charts.
  • Added hover styles for the TrackRowInfoVisLink visualization component, so that when a link area is hovered, a gray background rect and a text underline are also rendered.
  • Added a context menu to add a new track on top or bottom with selected rows in categorical bar charts.
  • Added viewWrapper react component that support view-specific interactions, such as brusing columns of higlas heatmaps.
  • Added an option to render a checkbox for each row of the data table, with a callback function that takes an array of checked row objects.
  • Added wrapper visualizations to SVGs exported by HiGlass using the new .on('createSVG') callback feature.

Changed

  • Fixed bug which prevented wrapper options for sorting, filtering, highlighting from being used upon initial component render.
  • Added resizer elements to their containers and used d3-drag for the mouse events.
  • Compute color scale for the TrackRowInfoVisNominalBar categorical value visualization based on the full rowInfo rather than transformedRowInfo so that the original color mapping is kept after row filtering events.
  • Fixed the genomic interval selection behavior to reflect the support for fromViewUid: null for viewport-projection-horizontal tracks (new in HiGlass 1.9.0).
  • Set the horizontal-multivec track zeroValueColor option to demonstrate the feature (new in HiGlass 1.9.0).
  • Enabled multiple genomic interval selections for a view.

0.1.0 - 02/19/20

Added

  • Added radio buttons for selecting between two higlass viewconfig options.
  • Added higlass viewconfig corresponding to local higlass-server demo tileset containing JSON metadata.
  • Configured documentation.
  • Added rollup configuration for packaging the component for NPM.
  • Display metadata values in tooltip upon mouse hover interactions for TrackRowInfo component.
  • Added TrackRowLink component, and implemented dynamic dimensions based on the rowLinkPosition option and dynamic show/hide based on row height. URLs are obtained based on the rowLinkAttribute option which defaults to "url".
  • Added TrackColTools component, shows a button for creating a genome interval selection, and can be positioned above or below horizontal-multivec tracks using the colToolsPosition option.
  • Added a dendrogram visualization to the TrackRowInfo component, which is displayed when type === "tree" for a row info attribute in the options prop.
  • Added a quantitative attribute visualization (vertical bar plot) to the TrackRowInfo component, which is displayed when type === "quantitative" for a row info attribute in the options prop.
  • Added buttons for sorting according to a particular attribute, which appear upon hovering over the visualization for the attribute in the TrackRowInfo component.
  • Added a new demo with a HiGlass viewconfig containing two horizontal-multivec tracks, where two sets of options for the wrapper component are specified based on the viewId and trackId of each track.
  • Added a mechanism for components to "register" their draw() functions, to prepare for drawing visualizations to SVG when the user would like to export the current visual state.
  • Added a global variable that stores rowInfo as well as sorting & highlighting info, using React.Context.
  • Added a mechanism to sort rows of a HiGrass horizontal-multivec track and vertical tracks on the left and right sides which is activated when users click on sorting buttons.
  • Added a feature to interactively highlight rows by typing keywords on a text field which appears when a search button is clicked.

Changed

  • Moved to rendering the row info categorical metadata on a single <canvas/> element, rather than colored HTML elements for each row.
  • Updated all d3 imports so that they refer to a specific sub-package (such as d3-selection or d3-scale).
  • Changed rollup config output.sourcemap values to true rather than "inline", which means that sourcemaps are stored in separate files, reducing the size of the .js files.
  • Updated the positioning of the genomic interval start and end coordinate elements, so that they are dynamically positioned based on the current genomic region in the track.
  • Added a small implementation of renderer-agnostic drawing code, based on the two.js JavaScript library, which enables the same code to draw to SVG and canvas elements. For example, when rendering in the browser, canvas is preferred for speed, but when rendering for export to a file, SVG is preferred for resolution.