Changelog

Source: NEWS.md

iSEE 2.19.1

• Changed the processing of the title for the app - if provided explicitly, now it can also correctly handle HTML content tags and more. Thanks to @RiboRings for spotting this, resolving #681

iSEE 2.17.4

• Add explicitly a “Stop app” button to close the application (should be a means to nicely behave in container-spawned instances). Addresses #630
• Fix text in ‘configure’ vignette. Closes #626
• Copy information from rowRanges to rowData Closes #637
• Require at least one valid value for atomic, groupable and numeric columns. Closes 660
• If heatmap matrix has no finite values, set the color range arbitrarily. Closes #610
• Limit the number of rows in heatmap annotation legends to 10. Closes #591
• Fix license. Closes #661.
• Rename some internal constants.
• Add checkbox to fix aspect ratio to 1. Closes #541.
• Add checkbox to hide violin boundaries. Closes #619.

iSEE 2.17.3

• Preserve the existing order of rows when receiving a selection in RowDataTable, ColumnDataTable panels.

iSEE 2.17.2

• Export function .selectInputHidden().

iSEE 2.17.1

• Fix typo in setMethod(".getContinuousMetadataChoices", "RowDotPlot", ...).

iSEE 2.15.1

• Add button ‘Draft out a tour’ to navigation bar.
• Add button ‘About this data set’ to navigation bar.

iSEE 2.13.5

• Add generic .isBrushable to support panels that are not DotPlot extensions.

iSEE 2.13.4

• Fix COLORMAP bug introduced in 2.13.3.

iSEE 2.13.3

• Let app maintainer define colormap in the landing page.

iSEE 2.13.2

• Fix bug introduced in 2.11.2 (DataBoxOpen would apply also to Visual parameters box)

iSEE 2.13.1

• Define missing methods for generics for custom tables (issues #608 and #612)

iSEE 2.11.4

• Fix bug introduced in 2.11.2.

iSEE 2.11.3

• Use standard syntax to include empty icon in relevant places (issue #606).

iSEE 2.11.2

• Make it possible to hide the “Visual Parameters” box (issue #611).

iSEE 2.11.1

• Add tooltip.signif to registerAppOptions() to regulate the number of significant digits shown in the tooltip.

iSEE 2.9.12

• Export constants used in iSEEu.

iSEE 2.9.11

• Fix R CMD check warnings about missing documentation.

iSEE 2.9.10

• Enable customisation of hovering tooltip in DotPlot panels including colData or rowData information.

iSEE 2.9.9

• Allow screenshots in vignettes to use full width of pkgdown site.

iSEE 2.9.8

• Enable autocompletion for feature names in the heatmap feature selection modal.

iSEE 2.9.7

• Update FontAwesome icon question-circle to circle-question (v6).

iSEE 2.9.6

• Bugfix related to https://github.com/rstudio/shiny/issues/3125, mainly applicable to custom landing pages that render a DT::datatable() prior to selectInput().

iSEE 2.9.5

• Bugfix reverting a change in 2.9.3 breaking re-rendering of reactivated panels.
• Complete bugfix to prevent unnecessary re-rendering of ComplexHeatmapPlot panel when dimension of an incoming multiple selection is dismissed by the options of the child panel.

iSEE 2.9.4

• Bugfix setting the active multi-selection info of Table panels to a fixed message, as the panel is not re-rendered when search boxes are used.
• Bugfix re-rendering ComplexHeatmapPlot panels when displaying incoming column selection.

iSEE 2.9.3

• Partial bugfix avoiding re-rendering of ComplexHeatmapPlot panel when an incoming row selection changes if custom rows are in use. The partial bugfix only applies if the ComplexHeatmapPlot also disables the restriction on any incoming column selection.

iSEE 2.9.2

• Document the existing panel modification modes.

iSEE 2.9.1

• Add spinner to ComplexHeatmapPlot.

iSEE 2.5.3

• Replace icons with fontawesome 5 versions

iSEE 2.5.2

• Bugfix for conversion of categorical columns with too many levels to numeric ones
• Bugfix for heatmap crashing if columns were ordered by a selection that was not shown

iSEE 2.5.1

• Bugfix for removed panels showing up among the selectable ones.

iSEE 2.3.14

• Allow modification of font sizes for row and column names in ComplexHeatmapPlot.
• Bugfix for assignment of annotation colors in ComplexHeatmapPlot.

iSEE 2.3.13

• Avoid partial name matching in .getCachedCommonInfo.
• Deprecated iSEEOptions in favor of panelDefaults (for construction-time globals) and registerAppOptions (for runtime globals).

iSEE 2.3.12

• Added an .allowableColorByDataChoices generic for downstream panels to control ColorBy*Data choices.

iSEE 2.3.11

• Cleaned up tours for Tables and the ComplexHeatmapPlot.

iSEE 2.3.10

• Document and export the .getDotPlotColorHelp utility.
• Bugfix for the RowDotPlot color tour.

iSEE 2.3.9

• Add a distributed tour attached to each individual UI element.
• Bugfix for ordering of selected columns in ComplexHeatmapPlot.

iSEE 2.3.8

• Use shiny::MockShinySession$new() to simulate Shiny session objects.

iSEE 2.3.7

• Bugfix for missing import of geom_density_2d

iSEE 2.3.6

• Bugfix for graceful deprecation of old parameters in various constructors.

iSEE 2.3.5

• Added functionality to use multiple row/column selections as a factor on the axes, for faceting or for coloring.
• Moved selection transparency setter into the “Visual parameters” box.
• Deprecated SelectionEffect="Color" in favor of ColorBy="Column selection" and ColorBy="Row selection".
• Deprecated SelectionColor as the coloring for selections is determined using colDataColorMap() instead.
• Deprecated SelectionEffect="Restrict" in favor of ColumnSelectionRestrict and RowSelectionRestrict.
• Deprecated ColumnSelectionType and ColumnSelectionSaved (ditto for rows) as all active/saved selections are now transmitted.

iSEE 2.3.4

• Fix wiring of button observer to open vignette.

iSEE 2.3.3

• Edge-case bugfix for correct cleaning of zero-row/column SummarizedExperiments.

iSEE 2.3.2

• Added the cleanDataset() generic to ensure all names in the SummarizedExperiment are present and unique.

iSEE 2.3.1

• Bugfix to the heatmap color selection for near-zero length ranges.

iSEE 2.1.27

• Minor edits to the API documentation.

iSEE 2.1.26

• Disable the import button on the dimnames modal when transmitter has not made a selection.
• Separate the maximum number of factor levels for colors from other applications.

iSEE 2.1.25

• Support a named vector in the SearchColumns field of the Table subclasses.

iSEE 2.1.24

• Enable custom saving of the application state via the new saveState= argument.
• Switch colormap getters to use an internal cache to avoid conflicts with user entries.

iSEE 2.1.23

• ExperimentColorMap inherits from Annotated.

iSEE 2.1.22

• Split and rename scripts for test setup.

iSEE 2.1.21

• Minor fix to unit test.

iSEE 2.1.20

• Export even more internal utilities for re-use in downstream packages.
• Minor fixes to the ComplexHeatmapPlot documentation.

iSEE 2.1.19

• Export more internal utilities for re-use in downstream packages.
• Added a generic to define the selection effect UI.
• Fixes to the ComplexHeatmapPlot observers, most obviously for the assay choice.
• Fixes to the underlying reactive framework to avoid bugs due to unresponsiveness.

iSEE 2.1.18

• Bugfix to properly support dynamic classes on landing page.

iSEE 2.1.17

• .refineParameters() for FeatureAssayPlot, SampleAssayPlot protects the x-axis choice against absent metadata.
• CSS classes for each panel are now defined at app run-time, to make it easier to write landing pages without specifying initial= in iSEE().

iSEE 2.1.16

• Bugfix for initialization of the ColorByFeatureDynamicSource UI element in ColumnDotPlots.

iSEE 2.1.15

• Allow labelling of the medoid for each level of a discrete variable in a scatter-type DotPlot.
• Turned on validity checks during [[<- assignment into Panel classes.

iSEE 2.1.14

• Right-aligned the help icon for individual panel tour.
• Added tooltip for mouseovers on DotPlot panels.
• Allowed custom annotation about selected table row to to be displayed in Table panels.

iSEE 2.1.13

• Refactored the heatmap feature selection modal to be reusable for selecting rows or columns in other contexts.

iSEE 2.1.12

• Added panel-specific tours via the .definePanelTour() generic.
• Generalized the HiddenColumns mechanism to all Table subclasses.

iSEE 2.1.11

• Added HiddenColumns slot to hide columns in ColumnDataTables and RowDataTables.

iSEE 2.1.10

• Avoided transmitting multiple selections for Tables when the number of columns change.
• Hid irrelevant UI elements for Table multiple selections.
• Generalized information about the number of selected rows/columns in each panel.
• Streamlined the .defineOutput signature.

iSEE 2.1.9

• Improved documentation for generics and classes.
• Defined .exportOutput method for the ComplexHeatmapPlot class.
• Added missing documentation for slots and methods in the ComplexHeatmapPlot class.
• Enforced sensible defaults for the dynamic selection setting.
• Extract assays with dimnames for correct indexing.

iSEE 2.1.8

• Fixed control of legend point size for continuous covariates.
• Extended control of legend point size for violin plots and Hinton plots.

iSEE 2.1.7

• Added control of legend point size under the “Text” category of the “Visual parameters” box.

iSEE 2.1.6

• Fixed bug for sizeBy observers.

iSEE 2.1.5

• Fixed initialization of panel size to current value when the “Organize panels” window is closed and re-opened.
• Fixed removal of last panel from the interface.

iSEE 2.1.4

• Added progress bar when exporting panel outputs.
• Fixed missing section in createLandingPage() man page.

iSEE 2.1.3

• Fixed handling of logical > 1 when processing the CustomRowsText slot in the ComplexHeatmapPlot constructor.

iSEE 2.1.2

• Added a new vignette to describe panel links.
• Fixed documentation for *DynamicSource slots.
• Fixed reception of single selection from plot at initialization.
• Removed deprecated functionality.

iSEE 2.1.1

• Added vignette documenting the use of out-of-memory matrices for big data.
• Added TENxPBMCData to Suggests:.

iSEE 1.99.9

• Fixed slot names in the ReducedDimensionPlot() man page.

iSEE 1.99.8

• Protected against transient invalid selected index; fixes #400.
• Forced renderDT to rerun expression upon panel reorg.

iSEE 1.99.7

• Fixed out-of-date vignette content.

iSEE 1.99.6

• Added static screenshots to vignettes.
• Added GitHub Actions for continuous integration and deployment.
• Updated Docker base image to bioconductor/bioconductor_docker:devel.

iSEE 1.99.5

• Export utilities relevant to downstream panel development.

iSEE 1.99.4

• Added options for dynamic choice of single/multiple selection sources.
• Fixed bug around NA groupings in subsetPointsByGrid().
• Explicitly notify the user when removing invalid panels supplied by a landing page.

iSEE 1.99.3

• Fixed occurrences of rowData in RowDotPlot panels.
• Refactored .create_visual_box().
• Refactored visual parameter sections into generics.
• Apply global option selected.color to single selections.
• Added panel.width, panel.height, and assay to global options.
• Added .checkboxInputHidden().

iSEE 1.99.2

• Added extension points to the API.
• Added global settings using iSEEOptions.
• Added .allowableYAxisChoices() and .allowableXAxisChoices() methods to intercept choices of x/y-axis variables.

iSEE 1.99.1

• Allowed customization of landing pages (from calling iSEE() in no-SE mode) for enterprise deployments.
• Allowed export of plot and table panel outputs as PDF and CSV files, respectively.
• Fixed handling of se objects missing dimnames.
• Added createCustomPlot() and createCustomTable() to provide on-ramp for making customized panels.
• Allowed global setting using iSEEOptions.
• Expanded class and slot names from “Feat” to “Feature”, “Samp” to “Sample”, “RedDimPlot” to “ReducedDimensionPlot”.
• Renamed “StatTable” to “DataTable”.

iSEE 1.99.0

• Refactored panel implementation as S4 classes.
• Display a spinner while panels are rerendering.
• Refactored heatmap panel to use ComplexHeatmap.

iSEE 1.7.2

• Added notification on birthday.
• Enabled hiding of the *DataPlot UI elements.

iSEE 1.7.1

• Fix rbind() of data.frame and DataFrame objects.
• Fix error related to using && with variable length greater than 1.
• Replace deprecated scater argument.
• Replace deprecated functions: SingleCellExperiment::clearSpikes(), SingleCellExperiment::clearSizeFactors().

iSEE 1.7.0

• Bioconductor release.

iSEE 1.5.13

• Order features selected in heat map selectize from top to bottom.

iSEE 1.5.12

• Support gene list input from aceEditor() and fileInput().

iSEE 1.5.11

• Renamed isColorMapCompatible() to checkColormapCompatibility().
• Fixed graceful server side handling of checkColormapCompatibility().
• Updated documentation about panel organisation in vignette.

iSEE 1.5.10

• Fixed test to provide a non-empty selection to custom plot function.

iSEE 1.5.9

• Introduced Bugs Easter egg.

iSEE 1.5.8

• Substituted deprecated scater::normalize() by scater::logNormCounts().

iSEE 1.5.7

• Simplified protection of redDimPlotDefaults() against empty reducedDims.
• Fix to declare all panel types not available.

iSEE 1.5.6

• Updates following deprecation of isSpike() and sizeFactorNames().

iSEE 1.5.5

• Added modeEmpty().
• Support zero-row initialPanels argument.

iSEE 1.5.4

• Added support for file upload with server re-initialization.
• Moved observers to separate file. Exclude from code coverage.
• Updated calls to ReprocessedAllenData() to load only tophat_counts assay.

iSEE 1.5.3

• Use ReprocessedAllenData() following the deprecation of data(allen).

iSEE 1.5.2

• Minor doc fix.
• Do not allow duplicated values in Name field of initialPanels.
• Downsample points randomly.

iSEE 1.5.1

• Fixed report of table links.

iSEE 1.5.0

• Bioconductor release.

iSEE 1.3.9

• Added ORCID identifiers.
• Fixed subscript error when tables receive a selection.
• Fixed panel names in panel organization selectize input.
• Control the application of panel organization updates using an action button.
• Fixed child replotting upon lasso close.
• Fixed code reporting for zero-length DataFrame.

iSEE 1.3.8

• Added support for multiple selections.
• Avoid Javascript error with check group conditional.

iSEE 1.3.7

• Added “ImmunoOncology” in biocViews.

iSEE 1.3.6

• Control point size.

iSEE 1.3.5

• Additional information during the default tour.

iSEE 1.3.4

• Fixed panel organization selectize.

iSEE 1.3.3

• Updated default tour steps to match updated user interface.
• Parsed quote symbols literally in default tour steps.
• Fixed name-to-index conversion of feature names for heat map panel.

iSEE 1.3.2

• Moved panel organization to modal with selectize to control panel display and ordering, remove sidebar.
• Added control of width and height of new panels.
• Enabled voice control.
• Refactored internal functions.

iSEE 1.3.1

• Fixed invalid row index sent from tables in RStudio browser.
• Fixed initialization of search fields for tables that are initialized with an incoming selection.
• Fixed constant field name.

iSEE 1.3.0

• Bioconductor release.

iSEE 1.1.14

• Fixed unit test.

iSEE 1.1.13

• Added missing observer for assay type in row data plot panels.
• Added missing observer for colorpicker when colouring by feature name in row-based plots, or by sample name in column-based plots.
• Ignore NA values when computing the range of coloring scales.
• Added a size expansion factor (5x) to the selected point when colouring by feature name in row-based plots, or by sample name in column-based plots.
• Fixed redundant coloring of selected point when colouring by feature name in row-based plots, or by sample name in column-based plots.
• Updated basic vignette.

iSEE 1.1.12

• Updated NEWS file.

iSEE 1.1.11

• Exported list of panel names and codes.

iSEE 1.1.10

• Fixed colour scale to be invariant when selecting on a different color.
• Protected heat map plot panels against restriction on zero samples.

iSEE 1.1.9

• Fixed compatibility with DelayedArray assays.

iSEE 1.1.8

• Extended unit test coverage.
• Moved generics to separate file.
• Minor fix to annotateEnsembl().
• Updated list of functionalities in README.

iSEE 1.1.7

• Resolved BiocManager message.

iSEE 1.1.6

• Minor fix for Windows unit test.

iSEE 1.1.5

• New panel colors.
• Added control for arguments to custom panels through action buttons.
• Distinguished visible from active arguments for custom panels.

iSEE 1.1.4

• Split ?defaults help page by panel type.
• Generalized support for custom data plots and statistics tables.

iSEE 1.1.3

• Added new Sample assay plot panel type.
• Extended documentation.
• Split vignette into three: basic, advanced, ExperimentColorMap.
• Fixed initialization of reduced dimensions with a single plot axis choice.
• Substituted discouraged use of sapply().
• Moved roxygen importFrom instructions closer to the relevant code.
• Increased unit test coverage.
• Consistent use of “colormap” through the package.
• Updated installation instructions.
• Added CITATION file.
• Added Figure 1 of article in README.

iSEE 1.1.2

• Enabled faceting by row and column, with appropriate updates to brush and lasso.
• Enabled shaping on data points.
• Minor fix of jitter for violin and square plots.
• INTERNAL: Enabled storage of additional plot.data beyond X and Y in all.coordinates. See constant .allCoordinatesNames. Necessary for correct behaviour of brushes on faceted plots.

iSEE 1.1.0

• Bioconductor release.

iSEE 1.0.1

• Renamed feature expression plots to feature assay plots, for generality.

iSEE 0.99.3

• Custom tours can be restarted via the dropdown menu button, overwriting the default tour.
• Added functionality to provide a custom title to be displayed in the app.
• Preserved data points and width ratio upon zoom on discrete variables.

iSEE 0.99.2

• Added functionality for providing additional custom tours, to be launched directly upon starting the app.

iSEE 0.99.1

• Added grid-based visual point downsampling for faster plotting, including control of resolution.
• Added button “Clear features” for heat maps.
• Reorganized buttons in heat map panels.
• Transferred maintainer badge to Federico.

iSEE 0.99.0

• Initial submission to Bioconductor.