Changes in version 1.12.2                        

  - Bug Fix: Allow 'dittoHeatmap()' to plot from pre-scaled data by
    fixing internal data check to actually look for non-zero values
    instead of a non-zero sum.

                       Changes in version 1.12.1                        

  - Bug Fix: Update 'getReductions()' to correctly return NULL when the
    'object' contains no dimensionality reductions.

                        Changes in version 1.12                         

  - No code updates. (Bioconductor version number update only)

                        Changes in version 1.10                         

  - Added ability to plot multiple 'var' in a single 'dittoPlot()',
    'dittoDimPlot()', 'dittoScatterPlot()', 'dittoDimHex()', and
    'dittoScatterHex()' call by giving a vector of genes or continuous
    metadata to the 'var' or 'color.var' input. Customization of how the
    "multivar" data is displayed can be controlled with: 1-
    'multivar.aes' (context: 'dittoPlot()' only) - which plot aesthetic
    is utilized for displaying var-values. 2- 'multivar.split.dir' -
    faceting direction to use for var-data when combining with an
    additional 'split.by' variable.
  - Improved the compatibility with 'split.by'/faceting customizations,
    specifically with 'split.adjust = list(scales = "free")', by making
    implementations of 'min'/'max' inputs less intrusive. Note: This
    change very minorly alters the default output of some plotters.
  - Improved error messaging for cases where 'object' does not have
    cell/column names.

                         Changes in version 1.8                         

  - Minor Feature Add: 'randomize' option for 'order' input of
    'dittoDimPlot()' and 'dittoScatterPlot()'

                         Changes in version 1.6                         

  - Vignette Update: Added a 'Quick-Reference: Seurat<=>dittoSeq'
    section.
  - Build & Test Infrastructure Update: Removed Seurat dependency from
    all build and test materials by removing Seurat code from the
    vignette and making all unit-testing of Seurat interactions
    conditional on both presence of Seurat and successful SCE to Seurat
    conversion.
  - Bug Fixes: 1- Fixed dittoFreqPlot calculation machinery to properly
    target all cell types but only necessary groupings for every sample.
    Removed the 'retain.factor.levels' input because proper calculations
    treat 'var'-data as a factor, and groupings data as non-factor. 2-
    Allowed dittoHeatmap() to properly 'drop_levels' of annotations by
    ensuring 'annotation_colors' is not populated with colors for empty
    levels which would be dropped. 3- Made 'do.label' machinery of
    scatter plots robust to NAs.

                         Changes in version 1.4                         

  - Added 1 new Visualization function: 'dittoFreqPlot()'.
  - Added interaction with 'rowData' of SE and SCEs via a
    'swap.rownames' input, e.g. to simplify provision of 'var's via
    symbols vs IDs.
  - Improved & expanded 'split.by' capabilities by: 1- adding them to
    'dittoBarPlot()', 'dittoDotPlot()', and
    'dittoPlotVarsAcrossGroups()'; 2- adding 'split.adjust' input to all
    functions for passing adjustments to underlying 'facet_grid()' and
    'facet_wrap()' calls; 3- adding 'split.show.all.others' input to
    'dittoDimPlot()' and 'dittoScatterPlot()' to allow the full spectrum
    of points, rather than just points excluded with 'cells.use', to be
    shown as light gray in the background of all facets; 4- Bug fix:
    splitting now works with labeling of Dim/Scatter plots, with label
    position calculated per facet, and without affecting facet order.
  - Improved 'dittoPlot()'-plotting engine (also effects
    'dittoPlotVarsAcrossGroups()', and 'dittoFreqPlot()') by: for y-axis
    plotting, 1- extended geom dodging to also work on jitters when
    'color.by' is used to add subgroupings & 2- added a
    'boxplot.lineweight' control option; for x-axis / ridge plotting, 1-
    added an alternative histogram-shaping option (Try 'ridgeplot.shape
    = "hist"') & 2- improved use of white space via a new
    'ridgeplot.ymax.expansion' input.
  - Standardized output logic so that 'do.hover = TRUE' will lead to
    plotly conversion even when 'data.out = TRUE'.
  - 'dittoHeatmap()': 'order.by' can also now accept multiple
    gene/metadata names to order by & bug fix: when given an integer
    vector, that vector will be used directly to set the order of
    heatmap columns.
  - 'dittoBarPlot()': grouping & 'var' order control improved via
    addition of a 'retain.factor.levels' input.

                         Changes in version 1.2                         

  - Added 3 New Visualization Functions, 'dittoDotPlot()',
    'dittoDimHex()' & 'dittoScatterHex()'.
  - Expanded SummarizedExperiment compatibility across the entire
    toolset.
  - Added ComplexHeatmap integration to 'dittoHeatmap()', controlled by
    a new input, 'complex'.
  - Added Rasterization for improved image editor compatibility of
    complex plots. (See the dedicated section in the vignette for
    details.)
  - Added 'labels.split.by' input & 'do.contour', 'contour.color', and
    'contour.linetype' inputs to scatter/dim-plots.
  - Added 'order' input to scatter/dim-plots for control of plotting
    order.
  - Added 'metas' input for displaying such data with 'dittoHeatmap()'.
  - Added 'adjustment' input to 'meta()', which works exactly as in
    'gene()' (but this is not yet implemented within data grab of
    visualiation functions).
  - Added 'adj.fxn' input to 'meta()' aand 'gene()' for added control of
    how data might be adjusted (but this is not yet implemented within
    data grab of visualiation functions).
  - Replaced (deprecated) 'highlight.genes' input with
    'highlight.features' in 'dittoHeatmap()'.
  - Replaced (deprecated) 'OUT.List' input with 'list.out' for all
    'multi_*' plotters.

                         Changes in version 1.0                         

  - Submitted to Bioconductor.