NEWS.md

In iSEE: Interactive SummarizedExperiment Explorer

iSEE 2.2.4

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

iSEE 2.2.3

• Bugfix for missing import of geom_density_2d

iSEE 2.2.2

• Fix wiring of button observer to open vignette.

iSEE 2.2.1

• 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 teh "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 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().

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.
• Transfered maintainer badge to Federico.

iSEE 0.99.0

• Initial submission to Bioconductor.

iSEE documentation built on Feb. 3, 2021, 2:01 a.m.