Changes in version 1.16
- Feature Extensions:
1. Multi-modality functionality: To support visualization of
markers from multiple modalities in the same plot, e.g. gene
expression by RNA and protein capture by ADT, the mechanics of
'assay', 'slot', and 'swap.rownames' inputs have been expanded,
although defaults are unchanged. See the '?GeneTargeting'
documentation page for details. For the standard Seurat CITEseq
case, set 'assay = c("RNA", "ADT")'.
2. 'dittoDotPlot()' vars-categories: Added support for
categorization of markers, as well as for x and y axes swapping.
- Provide 'vars' as a named list to group markers (list
element values) into categories (list element names).
- New input 'vars.dir' controls which axis is used for markers
("x" by default, or "y").
- New boolean inputs 'categories.theme.adjust' or
'categories.split.adjust' can be used to turn off associated
automated additions to the 'theme' input or 'split.adjust'
input as well as faceting mechanics, respectively.
3. 'dittoDotPlot()' 3-color scaling: Added support for injecting a
midpoint color to the color scale via 2 new inputs.
- New input 'mid.color' acts as the switch, and can be set to
the specific strings "ryb", "rwb", or "rgb" (g for gray
here) for a single-point quick update to use corresponding
ColorBrewer inspired scales (effectively updating
'min.color' and 'max.color' as well). 'mid.color' can
alternatively be given a color directly for more fine-grain
control of colors.
- New input 'mid' controls the data value at which 'mid.color'
will be used in the scale.
4. Additional data representation controls for all
'dittoPlot()'-style plotters, which includes 'dittoFreqPlot()':
- New input 'boxplot.outlier.size' allows control of the
outlier shape's size for "boxplot" representations.
- New input 'vlnplot.quantiles' allows addition of lines at
requested data quantiles for "vlnplot" representations.
5. Added a new built in 'color.method' style for
'dittoScatterHex()' and 'dittoDimHex()' plotters:
- When 'color.var' targets discrete data, giving 'color.method
= "prop.<value>"', where <value> is an actual data level of
'color.var'-data, will set coloring to represent the
proportion of <value> among the 'color.var'-data of each
bin.
6. New input 'labels.repel.adjust' allows finer control of the
'do.label' plot addition, via input pass-through to the geom
functions underlying labeling. This affects 'dittoDimPlot()',
'dittoScatterPlot()', 'dittoDimHex()', and 'dittoScatterHex()
functions.
- Bug Fixes:
1. 'dittoHeatmap()': Fixed a bug which blocked provision of
'annotation_row' and 'annotation_colors' inputs to
'dittoHeatmap()' without also generating column annotations via
either 'annot.by' or direct 'annotation_col' provision.
- Deprecation:
1. Completed deprecation of 'dittoHeatmap()'s 'highlight.genes'
input via removal from the function.
- Dependency Upkeep (generally invisible to users):
1. ggplot-v3: Replaced all calls to the deprecated 'aes_string()'
function with calls to the standard 'aes()' function. In cases
where mappings are successively built internally to accommodate
customization or flexibility, 'modifyList()' usage replaces the
previous simple 'list' and 'do.call()' management.
2. Seurat-v5: When the user's Seurat package version is 5.0 or
higher, conditional code switches expression data retrieval from
a call to the reportedly superseded 'GetAssayData()' function to
the newly supported 'SeuratObj[[<assay>]][<slot>]' syntax.
Changes in version 1.14
- Feature Extensions:
1. 'dittoDotPlot()' & 'dittoPlotVarsAcrossGroups()': Improved
'group.by' ordering control via retention of factor levels and
addition of a new 'groupings.drop.unused' input to control
retention of empty levels.
2. 'dittoHeatmap()': Targeting Seurat clusters with the "ident"
shortcut now works for the 'annot.by' input of 'dittoHeatmap()'.
- Bug Fixes:
1. 'dittoHeatmap()': Fixed a feature exclusion check in
'dittoHeatmap()' meant to remove features without any non-zero
values. Previously, it removed all features with a mean of zero,
which blocked plotting from pre-scaled data.
2. 'dittoDimPlot()' & 'getReductions()': Eliminated cases where
'getReductions()' did not return NULL for 'object's containing
zero dimensionality reductions. This fix also improves
associated error messaging of 'dittoDimPlot()' where such cases
were missed.
Changes in version 1.12
- No code updates. (Bioconductor version number updates 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.