NEWS

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CATALYST 1.29.2

• bug fix in 'clrDR' caused by 'calculateDR' failing when input is a 'table'

CATALYST 1.27.2

• fixed typos in man pages and vignette
• fixed unit test failures due to 'ggplot2'-updates etc.
• omit usage of ':::' operator throughout the package
• deprecate 'plotClusterHeatmap()' and 'plotMedExprs()' for good
• fixed 'ggplot2'-related messages/warnings (e.g., 'aes_string()' deprecation)

CATALYST 1.27.1

• bug fix in 'plotDiffHeatmap': add 'drop=FALSE' to avoid failure for DA when 1 cluster remains
• fix typos in differential vignette (issue #387)

CATALYST 1.27.0

• Bioconductor release 3.18

CATALYST 1.25.1

• fixed unit tests for differential plotting (expecting silence, but 'scater::calculateX' is throwing warnings related to argument 'useNames')

CATALYST 1.25.0

• Bioconductor release 3.17

CATALYST 1.23.5

• bug fix in 'ComplexHeatmap's: assure annotation colors show when 'sample_id's are not factors.
• fixed unit tests & examples
• added utility function to construct experimental design table from current SCE and avoid out-of-synch, e.g., after filtering
• comment: it took v1.23.3-.4 to pass builds & checks successfully

CATALYST 1.23.2

• fixed typos in vignette & documentation
• fixed bug in 'plotDiffHeatmap' examples & differential vignette

CATALYST 1.23.1

• updated 'ggplot2' syntax according to depracation
• fixed unit testing via 'set.seed' to avoid edge cases

CATALYST 1.20.1

• added argument 'dna' in normCytof() to allow specifying custom DNA channels
• prepData() now checks for & fixes panel discrepancies keeping the intersection/untion of channels according to 'fix_chs = "common / all"'
• in prepData(), exposed '...' arguments to be used by flowCore::read.FCS()
• added argument 'fix_chs'

CATALYST 1.18.1

• bug fix in plotPbExprs(): added 'drop = FALSE' in "DataFrame' subsetting

CATALYST 1.18.0

• Bioconductor 3.14 release

CATALYST 1.14.1 (2021-28-04)

preprocessing

• bug fix in computeSpillmat() when 'interactions = "all"'
• added unit tests for all combinations of 'interactions' and 'method'

CATALYST 1.12.2

preprocessing

• added argument 'FACS' to prepData(); dropping of non-mass channels can now be ommitted explicitly via setting FACS = TRUE
• allow coloring by clustering in plotScatter()

differential

• added new visualization clrDR() to plot low-dimensional embedding of centered log-ratios (CLR) on cluster-compositions across samples
• added argument 'assay' in plotExprs(), plotNRS() to allow specification of which assay data to use
• deprecated plotMedExprs() in favor of plotPbExprs() to allow flexibilty in input data and summary statistic, aggregating by cluster-sample (instead of by sample only), sizing by sample(-cluster) cell counts, and to specify whether to include (jittered) points, boxplots or both
• but fix in plotAbundances(); plotting failed when colData()$sample_id was not of type factor or character
• changed behavior of 'group_by' in plotAbundances(); not facetting the plot was previously impossible
• added arguments 'col_clust,distance,linkage' in plotAbundances() to allow sorting of samples according to hierarchical clustering on cluster compositions when by = "sample_id"

CATALYST 1.12.1

preprocessing

• bug fix in prepData(): by default, non-mass channels (time, event length etc.) are moved to the SCE's int_colData; forr FACS data, these are now kept inside the assay data (since FACS channels d+ not contain masses)

differential

• bug fix in plotFreqHeatmap(): frequencies were previously computed for the wrong margin (across clusters instead of samples); this has been fixed
• added checks in prepData() for the existence of md_/panel_cols to give a more intuitive error message when columns cannot be matched to the input md/panel
• added flexibility for pbMDS() to allow specification of - which assay data and summary statistic to use for aggregation - the level at which to aggregate (cluster, sample, cluster-sample)
• added vignette section "More - Exporting FCS files" on how to write FCS files from a SCE using sce2fcs()

CATALYST 1.12.0

preprocessing

• The daFrame class been removed and the preprocessing pipeline rewritten to use the SingleCellExperiment class instead. This greatly improves runtimes of debarcoding and normalization, and affects all functions associated with preprocessing: - normalization: normCytof() - debarcoding: assignPrelim(), est/applyCutoffs(), plotEvents/Yields() - compensation: computeSpillmat(), compCytof(), plotSpillmat()
• concatFCS() has been replaced by prepData(), which is used during differential analysis and already provided most of concatFCS()'s functionality. It has been adapted to - not require input panel and metadata tables (arguments 'panel' and 'md') - fix event times in the Time channel as was done previously by concatFCS() - reorder samples according to their acquisiton time when 'md' is unspecified
• sce2fcs() has been added to allow for easy conversion from SCE to flowFrame/Set, which can inturn be written to FCS file(s) - the SCE can be split into separate frames by a cell metadata variable (argument 'split_by') to, e.g., write debarcoded samples to separate files - any cell metadata and dimensionality reductions stored in the SCE can be optionally included in the output (arguments 'keep_cd' and 'keep_dr')
• plotScatter() has been added to support basic visualization of biscatters, but is not meant to compete with other tools available that were designed specifically for this task (namely, ggcyto) - cells my be colored by - density, in which case cells are binned via geom_hex() - a continuous or categorical cell metadata variable - facetting is flexible and allows to plot - one channel against a set of others - a pair of channels split by tw+ variables - one channel against others split by one variable
• plotYields() & plotSpillmat no-longer support interactive plotting with 'plotly'; this did not seem necessary and avoids additional dependencies
• plotEvents() & plotYields() now support specification of both, output directory and file name, via arguments 'out_path/name'

differential

• The metadata()$experiment_inf+ slot is constructed by prepData() and subsetted by filterSCE() as before. However, it is n+ longer required for any of the plotting functions associate with differential analysis. Instead, these rely only on the existence of the colData()$sample_id (and, for some, colData()$cluster_id) slot(s)
• Throughout all plotting functions, options for customizing visualizations (e.g., providing custom color palettes for heatmaps and clusters, turning on/off row/column clustering and dendrograms in heatmaps etc.) have been added
• plotCounts() previously only supported plotting absolute cell counts by sample and now allows to i) plot relative abundances (frequencies) instead; and, ii) group cell counts/frequencies by an addition cell metadata variable (e.g., to plot abundances split by both sample and patient ID)
• plotMDS() has been replaced by pbMDS() to avoid Namespace clash with scater::plotMDS()
• plotDR() failed to visualize PCA results; this has been fixed
• plotDR() now allows to visualize dimension reductions colored by an arbitrary number of markers with a single command
• plotClusterHeatmap() has been deprecated and replaced by - plotExprHeatmap() for pseudobulk expression heatmaps (by sample, cluster, cluster-sample) - plotFreqHeatmap() for relative cluster abundance heatmaps - plotMultiHeatmap() to combine pseudobulk expression & cluster frequency heatmaps side-by-side
• The vignette has been extended to include sections on how - ggplot2 & ComplexHeatmap visualizations can be customized or modified in retrospect - any clustering algorithms other than FlowSOM can be applied and incorporated to make use of the visualizations available in CATALYST - arbitrary ComplexHeatmap outputs from plotExprs/FreqHeatmap() can be combined manually, when not plotMultiHeatmap()
• An additional vignette has been added demonstrating how CATALYST's visualizations can be used with other data types from, e.g., scRNA-seq