Change exprs_values (and similar) to assay.type.
Tweak colouring of violin plots.
Fix use of block arguments in plotGroupedHeatmap.
Add scattermore and binning support to various plots (eg plotReducedDim).
swap_rownames works in retrieveCellInfo for
altExp now as well as in the main assay.
Add point_shape argument to plotDots and
plotPlatePosition.
Add projectReducedDim function to project points into
an existing reduced dimensionality embedding.
Support "color" and "colour" spellings in all plotting functions.
Add order_by argument to cellwise plot functions.
Add rasterise argument to plotReducedDim using
rasterise.
Add use_densvis argument to runTSNE to add densvis support in UMAP and TSNE embeddings.
Make multiplot defunct, remove deprecated args in plotHeatmap,
plotDots.
Add point_fun argument to plotColData and
plotExpression determine the geom used to draw cells in those plots.
Remove diffusion map functions that relied on destiny.
Add point.padding,force args to plotReducedDim; passed to geom_text_repel.
Add warning about unused use_dimred argument in runTSNE.
Rename colour_columns_by in plotHeatmap to
color_columns_by to match other arguments.
Add color_rows_by and row_annotation_colors arguments
to plotHeatmap, similar to analogous column arguments.
Change text_by annotations in plotReducedDim to use
geom_text_repel from ggrepel.
runMDS can use user-supplied function for calculating the
distance matrix. runMDS can optionally store the distance matrix
computed. runMDS also stores the eig and GOF fields
of the object returned.
Made the handling of center, scale, color and limits similar in plotDots, plotHeatmap, and plotGroupedHeatmap
Add use_fitsne argument to runTSNE allowing the use of fast interpolated t-SNE in place of Barnes-Hut t-SNE.
Migrated many utilities to the scuttle package.
Deprecated multiplot() in favor of gridExtras::grid.arrange().
Added swap_rownames argument to plot functions, allowing selection of genes using a rowData column.
Added column_annotation_colors argument to plotHeatmap
Changed default point aesthetics for all plots.
For runColDataPCA, reverted to documented behaviour of performing outlier detection on PCA coordinates rather than on non-transformed colData.
Added coldata_merge= argument to aggregateAcrossCells() for custom column metadata aggregation. Also include averaged reduced dimension results for each group.
Added label_format= argument to plotReducedDim() for greater control over the axis labels.
Added geometric= argument to librarySizeFactors() to compute size factors with a geometric mean.
Added the runMultiUMAP() function to perform a combined UMAP on multiple feature sets.
Added the medianSizeFactors() function to perform a DESeq2-like size factor calculation.
Modified isOutlier() so that min_diff= now acts on the log2 scale when log=TRUE. Added share_medians=, share_mads= and share_missing= options for sharing information across batches.
Exposed various developer utilities for downstream packages.
Modified sumCountsAcrossCells() to always return a SummarizedExperiment object, regardless of the class of ids. Return the number of cells used for summation in the colData.
Restored capability to create a data.frame from a SCE with makePerCellDF() and makePerFeatureDF().
Added ggcells() and ggfeatures() for convenient creation of ggplot objects from a SCE.
Removed deprecated dplyr verbs.
Removed deprecated method= option in runPCA(). Increased ncomponents= default to 50. Deprecated use_coldata= and related options in favour of runColDataPCA(). Switched BSPARAM= default to bsparam().
Added runColDataPCA() function for running PCA on colData(). Switch outlier detection strategy to avoid mvoutlier's dependency tree.
Added the annotateBMFeatures() function to perform annotation without modifying the input.
Pass all ... options to biomaRt::useMart() in getBMFeatureAnnos().
Added name= arguments to runPCA(), etc. to change the name of the output reducedDim.
Added the logNormCounts() function to compute log-normalized counts in an alternative experiment-aware manner. Added a normalization-by-downsampling option via DropletUtils.
Added the perCellQCMetrics() function to compute per-cell QC metrics in an alternative experiment-aware manner.
Deprecated the normalize() method, which was considered too vague to describe what the function was actually doing.
Added the perFeatureQCMetrics() function to compute per-feature QC metrics.
Deprecated the calculateQCMetrics() function, to be replaced by the streamlined addQCPerCell() and addQCPerFeature().
Generalized all functions, where possible, to operate on SummarizedExperiment and numeric matrices. This involved converting a number of them to S4 methods to take advantage of dispatch. Affected functions include normalizeCounts(), calculateCPM(), librarySizeFactors() and so on.
Added calculateTSNE() and related methods to operate directly on an input matrix.
Renamed the use_dimred= argument to dimred=, along with similar renamings of other arguments for consistency.
Report all percentages of variances explained as actual variances in runPCA() and getVarianceExplained().
Added aggregateAcrossCells() and aggregateAcrossFeatures() to create a summed SingleCellExperiment object.
Added the mockSCE() function to generate example objects for the documentation.
Support multiple factors for grouping cells in sumCountsAcrossCells().
Support list of grouping vectors in sumCountsAcrossFeatures().
Added the order_columns_by= argument to plotHeatmap() for easy plotting by a given factor. Changed defaults to more common values.
Added a plotDots() function to create a Seurat-style dot plot.
Dropped default nmads= to 3 in isOutlier().
Removed all functions deprecated in the last release.
Added option in runTSNE() to perform an external nearest neighbors check with BiocNeighbors. Removed the deprecated rand.seed= argument.
Added text_by= and related options to plotReducedDim(), to overlay annotation labels onto the plot.
Switched to BSPARAM= from BiocSingular for controlling SVD parameters. Deprecated the approximate= argument for runPCA().
Switched runUMAP() to use uwot::umap. Added support for supplying a pre-defined set of nearest neighbors.
Deprecated the various dplyr verbs, i.e., filter(), arrange(), mutate(), rename().
Fixes to all violin plots to ensure scatter matches up with violin outlines.
Rectangle categorical/categorical plots collapse to mirrored bar plots when either factor contains only one level.
Removed scater_gui(), downsampleCounts(), read10xResults(), normalizeExprs().
Simplified plotRLE() to avoid the need for internal faceting.
Added option for row subsetting in librarySizeFactors().
Ensured calcAverage() with subset_row= behaves as if the matrix was subsetted prior to the function call. Added support for parallelization.
Ensured calculateCPM() with subset_row= behaves as if the matrix was subsetted prior to the function call.
Added support for parallelization in nexprs().
Added readSparseCounts() for creating a sparse matrix from a dense array on file.
Added normalizeCounts() for easy division of matrix columns by the size factors. Modified to throw error upon encountering negative, NA or zero size factors.
Added preserve_zeroes= option to normalizeSCE() for preserving sparsity with non-unity pseudo-counts.
Added runUMAP() and plotUMAP() to use the UMAP dimensionality reduction method.
Added plotExplanatoryPCs() and getExplanatoryPCs() to correlate PCs with known factors. Deprecated findImportantPCs().
Added getVarianceExplained() to get the variance in gene expression explained by known factors.
Removed runKallisto() and runSalmon().
Switched readTxResults() to use tximport. Switched readSalmonResults() and readKallistoResults() to use readTxResults().
Removed obsolete fields in calculateQCMetrics(). Moved processing into C++ for a single-pass algorithm. Supported parallelization across cells for QC computations.
Added sumCountsAcrossFeatures() to sum counts across multiple redundant features. Deprecated summariseExprsAcrossFeatures().
All plotting functions can now access internal fields by using a character vector with NA as the first element.
Returned threshold values in the attributes of the output from isOutlier().
Deprecated the ticks in plotReducedDim().
Refactored calculateQCMetrics() to ignore potential non-linearity, rank genes by highest expression, rename automatically generated union sets, allow for output of a compact format.
Refactored all plotting functions to allow access to nested fields in the colData() or rowData(), by supplying a character vector.
Refactored plotTSNE(), plotPCA(), etc. to dispatch to the calculation functions (e.g., runTSNE(), runPCA()), with argument checks.
Refactored plotColData() and plotRowData() to use the same argument types as other functions rather than aes= input.
Removed all plotting functions that do not operate on SingleCellExperiment objects.
Deprecated read10xResults(), downsampleCounts() in favour of methods from the DropletUtils package.
Deprecated scater_gui() in favour of methods from the iSEE package.
Deprecated normalizeExprs() as this function made very little sense.
Added plotHeatmap() function, for easy plotting of heatmaps.
Added librarySizeFactors() function, to compute size factors from library sizes.
Added by_exprs_values= argument to many plotting functions, to distinguish direct plotting of expression values from their use in aesthetics.
Renamed arguments in plotHighestExprs(), plotExprsVsTxLength(), plotExprsFreqVsMean() for greater clarity.
Added centreSizeFactors() function for centralized size factor centering.
Added size_factor_grouping= argument to normalizeSCE(), calcAverage() and calculateCPM().
Added subset_row= argument to calculateCPM().
Consolidated size_factors= argument into use_size_factors= for calcAverage(), calculateCPM().
Modified normalizeSCE() so that centre_size_factors=FALSE does not use centred size factors at all during normalization.
Complete refactoring of the package to use the SingleCellExperiment class.
plotRLE() function to make relative log expression plots to assess and compare normalizations.
Refactored newSCESet() with defined hierarchy of data types
read10XResults() to read in results from 10x Chromium CellRanger output.
Refined QC metrics.
Bug fixes, efficiency improvements and more tests.
Key code ported to C++ for greater computational and memory efficiency
Added support/integration for SC3 package for single-cell clustering
writeSCESet() function added to write SCESets to HDF5 format on disk
mergeSCESet() function to merge two SCESet objects that share features
plotPlatePosition() function to visualise gene expression and cell metadata for cells in their position on a plate
Adding plotExprsVsTxLength() to plot expression against transcript length
Added fitted line and some tweaks to plotExprsFreqVsMean().
Adding support for scaled TPM counts when summarising expression at feature level.
Adding NULL method for set_exprs(). Adding tests.
Adding import of effective feature lengths with readKallistoResults()
runSalmon() function for running Salmon from within R, following suggestions from Rob Patro.
Added cellNames<- assignment function
Added extra QC metrics
Numerous other bug fixes and minor improvements
Package added to Bioconductor
Bioc-submission branch merged with master