Changes in version 2.5.3 - Replace icons with fontawesome 5 versions Changes in version 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 Changes in version 2.5.1 - Bugfix for removed panels showing up among the selectable ones. Changes in version 2.3.14 - Allow modification of font sizes for row and column names in ComplexHeatmapPlot. - Bugfix for assignment of annotation colors in ComplexHeatmapPlot. Changes in version 2.3.13 - Avoid partial name matching in .getCachedCommonInfo. - Deprecated iSEEOptions in favor of panelDefaults (for construction-time globals) and registerAppOptions (for runtime globals). Changes in version 2.3.12 - Added an .allowableColorByDataChoices generic for downstream panels to control ColorBy*Data choices. Changes in version 2.3.11 - Cleaned up tours for Tables and the ComplexHeatmapPlot. Changes in version 2.3.10 - Document and export the .getDotPlotColorHelp utility. - Bugfix for the RowDotPlot color tour. Changes in version 2.3.9 - Add a distributed tour attached to each individual UI element. - Bugfix for ordering of selected columns in ComplexHeatmapPlot. Changes in version 2.3.8 - Use shiny::MockShinySession$new() to simulate Shiny session objects. Changes in version 2.3.7 - Bugfix for missing import of geom_density_2d Changes in version 2.3.6 - Bugfix for graceful deprecation of old parameters in various constructors. Changes in version 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. Changes in version 2.3.4 - Fix wiring of button observer to open vignette. Changes in version 2.3.3 - Edge-case bugfix for correct cleaning of zero-row/column SummarizedExperiments. Changes in version 2.3.2 - Added the cleanDataset() generic to ensure all names in the SummarizedExperiment are present and unique. Changes in version 2.3.1 - Bugfix to the heatmap color selection for near-zero length ranges. Changes in version 2.1.27 - Minor edits to the API documentation. Changes in version 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. Changes in version 2.1.25 - Support a named vector in the SearchColumns field of the Table subclasses. Changes in version 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. Changes in version 2.1.23 - ExperimentColorMap inherits from Annotated. Changes in version 2.1.22 - Split and rename scripts for test setup. Changes in version 2.1.21 - Minor fix to unit test. Changes in version 2.1.20 - Export even more internal utilities for re-use in downstream packages. - Minor fixes to the ComplexHeatmapPlot documentation. Changes in version 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. Changes in version 2.1.18 - Bugfix to properly support dynamic classes on landing page. Changes in version 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(). Changes in version 2.1.16 - Bugfix for initialization of the ColorByFeatureDynamicSource UI element in ColumnDotPlots. Changes in version 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. Changes in version 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. Changes in version 2.1.13 - Refactored the heatmap feature selection modal to be reusable for selecting rows or columns in other contexts. Changes in version 2.1.12 - Added panel-specific tours via the .definePanelTour() generic. - Generalized the HiddenColumns mechanism to all Table subclasses. Changes in version 2.1.11 - Added HiddenColumns slot to hide columns in ColumnDataTables and RowDataTables. Changes in version 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. Changes in version 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. Changes in version 2.1.8 - Fixed control of legend point size for continuous covariates. - Extended control of legend point size for violin plots and Hinton plots. Changes in version 2.1.7 - Added control of legend point size under the "Text" category of teh "Visual parameters" box. Changes in version 2.1.6 - Fixed bug for sizeBy observers. Changes in version 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. Changes in version 2.1.4 - Added progress bar when exporting panel outputs. - Fixed missing section in createLandingPage() man page. Changes in version 2.1.3 - Fixed handling of logical > 1 when processing the CustomRowsText slot in the ComplexHeatmapPlot constructor. Changes in version 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. Changes in version 2.1.1 - Added vignette documenting the use of out-of-memory matrices for big data. - Added TENxPBMCData to Suggests:. Changes in version 1.99.9 - Fixed slot names in the ReducedDimensionPlot() man page. Changes in version 1.99.8 - Protected against transient invalid selected index; fixes #400. - Forced renderDT to rerun expression upon panel reorg. Changes in version 1.99.7 - Fixed out-of-date vignette content. Changes in version 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. Changes in version 1.99.5 - Export utilities relevant to downstream panel development. Changes in version 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. Changes in version 1.99.3 - Fixed occurences 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(). Changes in version 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. Changes in version 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". Changes in version 1.99.0 - Refactored panel implementation as S4 classes. - Display a spinner while panels are rerendering. - Refactored heatmap panel to use ComplexHeatmap. Changes in version 1.7.2 - Added notification on birthday. - Enabled hiding of the *DataPlot UI elements. Changes in version 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(). Changes in version 1.7.0 - Bioconductor release. Changes in version 1.5.13 - Order features selected in heat map selectize from top to bottom. Changes in version 1.5.12 - Support gene list input from aceEditor() and fileInput(). Changes in version 1.5.11 - Renamed isColorMapCompatible() to checkColormapCompatibility(). - Fixed graceful server side handling of checkColormapCompatibility(). - Updated documentation about panel organisation in vignette. Changes in version 1.5.10 - Fixed test to provide a non-empty selection to custom plot function. Changes in version 1.5.9 - Introduced Bugs Easter egg. Changes in version 1.5.8 - Substituted deprecated scater::normalize() by scater::logNormCounts(). Changes in version 1.5.7 - Simplified protection of redDimPlotDefaults() against empty reducedDims. - Fix to declare all panel types not available. Changes in version 1.5.6 - Updates following deprecation of isSpike() and sizeFactorNames(). Changes in version 1.5.5 - Added modeEmpty(). - Support zero-row initialPanels argument. Changes in version 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. Changes in version 1.5.3 - Use ReprocessedAllenData() following the deprecation of data(allen). Changes in version 1.5.2 - Minor doc fix. - Do not allow duplicated values in Name field of initialPanels. - Downsample points randomly. Changes in version 1.5.1 - Fixed report of table links. Changes in version 1.5.0 - Bioconductor release. Changes in version 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. Changes in version 1.3.8 - Added support for multiple selections. - Avoid Javascript error with check group conditional. Changes in version 1.3.7 - Added "ImmunoOncology" in biocViews. Changes in version 1.3.6 - Control point size. Changes in version 1.3.5 - Additional information during the default tour. Changes in version 1.3.4 - Fixed panel organization selectize. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 1.3.0 - Bioconductor release. Changes in version 1.1.14 - Fixed unit test. Changes in version 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. Changes in version 1.1.12 - Updated NEWS file. Changes in version 1.1.11 - Exported list of panel names and codes. Changes in version 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. Changes in version 1.1.9 - Fixed compatibility with DelayedArray assays. Changes in version 1.1.8 - Extended unit test coverage. - Moved generics to separate file. - Minor fix to annotateEnsembl(). - Updated list of functionalities in README. Changes in version 1.1.7 - Resolved BiocManager message. Changes in version 1.1.6 - Minor fix for Windows unit test. Changes in version 1.1.5 - New panel colors. - Added control for arguments to custom panels through action buttons. - Distinguished visible from active arguments for custom panels. Changes in version 1.1.4 - Split ?defaults help page by panel type. - Generalized support for custom data plots and statistics tables. Changes in version 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. Changes in version 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. Changes in version 1.1.0 - Bioconductor release. Changes in version 1.0.1 - Renamed feature expression plots to feature assay plots, for generality. Changes in version 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. Changes in version 0.99.2 - Added functionality for providing additional custom tours, to be launched directly upon starting the app. Changes in version 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. - Transfered maintainer badge to Federico. Changes in version 0.99.0 - Initial submission to Bioconductor.