NEWS.md

Release notes

AcidPlots 0.7.3 (2024-03-27)

Minor changes:

• Reworked plotCorrelation function.

AcidPlots 0.7.2 (2023-12-04)

Minor changes:

• plotCounts, plotCountsPerBiotype: Fixed unwanted type mismatch during internal leftJoin operations for SingleCellExperiment method.

AcidPlots 0.7.1 (2023-10-05)

Minor changes:

• plotCountsCorrelation: Add back xName and yName arguments, which are useful for customizing the plot labels.

AcidPlots 0.7.0 (2023-10-04)

Major changes:

• Now enforcing strict camel case for all function names.
• Renamed plotPCA to plotPca. Now using AcidGenerics variant instead of BiocGenerics here.
• Renamed plotQC to plotQc.
• Renamed plotTSNE to plotTsne.
• Renamed plotUMAP to plotUmap.
• Removed stringr dependency.

AcidPlots 0.6.1 (2023-08-17)

Major changes:

• All custom ggplot2 functions are now prefixed with acid_, for consistency.
• Simplified acid_coord_flip as acid_discrete_coord_flip. This no longer attempts to parse the gg object, and returns ggproto, so it can be chained in + operations.
• Renamed scale functions to fit ggplot2 snake_case conventions: autoContinuousColorScale to acid_scale_color_continuous; autoContinuousFillScale to acid_scale_fill_continuous; autoDiscreteColorScale to acid_scale_color_discrete; autoDiscreteFillScale to acid_scale_fill_discrete.

Minor changes:

• Removed usage of BiocParallel.

AcidPlots 0.6.0 (2023-08-11)

Major changes:

• Now requiring R 4.3 / Bioconductor 3.17.
• Reworked internal code to use rlang pronouns (.data) instead of legacy syntactic sugar approach with !! and sym. Refer to rlang documentation for details on non-standard evaluation and tidy evaluation.

Minor changes:

• Updated ggplot2 deprecations related to recommendation of linewidth instead of size for line geoms.
• plotCountsPerCell: Hardened point mode for SCE objects that don't contain precalculated nCount metadata in colData. Also improved error message when user attempts to plot point with a geom other than ecdf.
• plotCorrelation: Now using recommended after_stat instead of deprecated stat function for correlation calculations.

AcidPlots 0.5.5 (2023-04-27)

• NAMESPACE fixes for Bioconductor 3.17 compatibility.
• Now classing on DFrame instead of DataFrame virtual class.

AcidPlots 0.5.4 (2023-02-09)

• Updated dependencies to Bioconductor 3.16.
• Migrated requireNamespaces import from AcidBase to goalie.

AcidPlots 0.5.3 (2022-11-09)

Minor changes:

• Updated R dependency versions.
• Hardened internal calls to facet_wrap by using vars consistently. This requires calling sym with !! or syms with !!! (from rlang).

AcidPlots 0.5.2 (2022-10-25)

Minor changes:

• Improved dependency pinning, in anticipation of breaking changes introduced in basejump package updates, notably pipette and AcidExperiment.

AcidPlots 0.5.1 (2022-05-24)

Minor changes:

• Updated lintr checks and testthat unit tests.

AcidPlots 0.5.0 (2022-05-06)

Major changes:

• Starting a new release series that provides compatibility with R 4.2 and Bioconductor 3.15.

Minor changes:

• Removed internal dependencies on tibble (e.g. as_tibble coercion).

AcidPlots 0.4.0 (2022-03-11)

Major changes:

• Now using patchwork package internally for grid layout instead of cowplot.
• plotUpset: Now using ComplexUpset engine interanlly.

Minor changes:

• matchLabels: Simplified argument matching using new argName approach instead of legacy choices approach. Also improved hardening against mismatched user input, when attempting to specify elements in labels list that are not allowed/supported internally in the function.

AcidPlots 0.3.9 (2021-08-09)

Minor changes:

• matchLabels: Now allowing input of logical(1), so we can better support dynamic automatic plot labels.

AcidPlots 0.3.8 (2021-07-27)

Minor changes:

• acid_geom_label_repel: Now setting max.overlaps = Inf internally, to ensure that all points are always labeled. Refer to ggrepel examples documentation for details on max.overlaps argument, and the override option ggrepel.max.overlaps, which works globally in an R session.

AcidPlots 0.3.7 (2021-06-29)

Minor changes:

• Documentation improvements. In particular, split out documentation for our customized ggplot2 layer functions, which were previously documented (albeit in a somewhat confusing manner) in geoms.Rd file.
• Updated basejump and plotting dependency packages.
• Updated internal guides() handling to use character string instead of logical (e.g. FALSE), which was changed in ggplot 3.3.5+.

AcidPlots 0.3.6 (2021-05-17)

Major changes:

• plotCorrelation: Updated data.frame method to support labelCol, which is useful for defining the column to use for plot labels.
• plotCorrelation: The trans now defaults to "log10", instead of "identity". This is recommended for IC50 plots, which are the intended use of this function the majority of the time.

Minor changes:

• Updated dependencies to latest versions available on conda.
• Removed RColorBrewer and matrixStats as dependencies.

AcidPlots 0.3.5 (2021-03-12)

Minor changes:

• Removed unnecessary stringr dependency, since these functions are now reexported inside basejump.

AcidPlots 0.3.4 (2021-03-02)

Minor changes:

• Ensure we reexport percent from scales, which is used in pointillism.

AcidPlots 0.3.3 (2021-02-16)

Minor changes:

• Reexporting rlang functions that allow for standard evaluation within ggplot object creation: !!, !!!, sym, and syms.
• Removed need to use Matrix::colSums internally. Just inherit from the regular S4 generic.

AcidPlots 0.3.2 (2021-02-10)

Minor changes:

• Including some reexports that are used in DESeqAnalysis: draw_plot, ggdraw, log_breaks, plot_grid, and pretty_breaks.

AcidPlots 0.3.1 (2021-02-09)

New functions:

• plotCorrelation: Quick X-Y correlation scatterplot that calculates the R2 value, similar to plots in GraphPad Prism.

Minor changes:

• plotWaterfall: Reworked internal code to better handle splitting out of interesting groups into separate plots.
• Added initial SummarizedExperiment method support to plotWaterfall.
• Bug fixes to avoid issues with hard-coding sampleID internally as sample identifier column, helping improve migrate to sampleId as preferred method.
• Package no longer attaches basejump.

AcidPlots 0.3.0 (2020-10-07)

• Renamed package from acidplots to AcidPlots.

acidplots 0.2.36 (2020-09-02)

Minor changes:

• plotCounts: Added an assert to check for user attempting to use bar geom with style = "wide". Also added sort argument, which allows the user to easily plot the genes alphabetically instead of by vector order.

acidplots 0.2.35 (2020-09-01)

Minor changes:

• plotCounts: Added geom argument to support additional visualization types other than dots. Can now plot boxplot, violin, or bar plot.

acidplots 0.2.34 (2020-08-25)

Minor changes:

• plotHeatmap: Improved internal factor and NA handling of pheatmap annotation metadata, which can otherwise cause some legends to not render correctly. Note that we're ensuring factors get releveled correctly here.

acidplots 0.2.33 (2020-08-25)

Major changes:

• plotUpset: reworked default formals to now include nIntersects and orderBySize arguments. Improved internal argument handling and assert checks, ensuring user is passing in an integer matrix containing only 0,1 values. Improved the data.frame method to drop non-0,1 columns automatically, which supports the UpSetR movies working example.
• plotPCA: Reworked subtitle and title formals to instead use the standardized labels approach instead. Now automatically plots the number of genes used, which defaults to the top 500 most variable.

Minor changes:

• Updated default color and fill arguments to inherit better from ggplot2 defaults: scale_colour_continuous and scale_colour_discrete. The defaults still inherit from acid.color.continuous and acid.color.discrete first but then fall back to the ggplot2 default global options ggplot2.continuous.colour and ggplot2.discrete.colour.

acidplots 0.2.32 (2020-08-05)

Minor changes:

• Now using cli package for improved message appearance.

acidplots 0.2.31 (2020-08-05)

Minor changes:

• plotUpset: Adjusted ratio of dot matrix to main barplot, to handle complex multiple comparisons better.

acidplots 0.2.30 (2020-07-23)

Minor changes:

• Updated minimum R dependency to 4.0.
• plotUpset: Added matrix and list method support. Simplified internal code, reducing dependencies from UpSetR. Maybe consider switching to ggupset in a future update.

acidplots 0.2.29 (2020-07-09)

Minor changes:

• plotWaterfall: Now supports log transformations, defaulting to log10. Labels are disabled by default, and now only supported for non-log plots. For log transformed data, a line is now shown at the y intercept.

acidplots 0.2.28 (2020-06-25)

New functions:

• plotWaterfall: Easily plot concentration curve (e.g. IC50) waterfall plots.

acidplots 0.2.27 (2020-06-10)

Minor changes:

• matchLabels now returns an empty list for a NULL argument. This approach is used in the upcoming pointillism update, in the plotStackedBarPlot function.

acidplots 0.2.26 (2020-04-21)

Minor changes:

• plotCounts, plotHeatmap, plotQuantileHeatmap: Added convertGenesToSymbols support to override automatic mapping of genes to symbols, which is enabled by default.
• plotHeatmap, plotQuantileHeatmap: Improved showRownames handling for automatic visualization of rows, which are now enabled by default for heatmaps with <= 50 features.

acidplots 0.2.25 (2020-04-13)

Minor changes:

• Updated documentation and roxygen dependency to v7.1.0.
• Updated ggplot2 and other graphical R package dependencies.
• Fixed plotHeatmap unit tests to harden against SummarizedExperiment and SingleCellExperiment objects defined in AcidTest package that contain rows and/or columns with all zeros. Refer to nonzeroRowsAndCols function in basejump for details.
• Rebuilt pkgdown website using v1.5 update.

acidplots 0.2.24 (2020-03-11)

Minor changes:

• acid_coord_flip: Fix for breaking change introduced by ggplot2 v3.3.0, which renamed object[["layers"]][[1L]][["geom"]][["required_aes"]] from "x" to "x|y". The package now requires this new version of ggplot2.

acidplots 0.2.23 (2020-02-22)

Minor changes:

• Changed license from MIT to GPL-3.
• Updated internal code to use aggregateCellsToSamples instead of pseudobulk, which has migrated to pointillism and will be reworked in an upcoming release.
• Updated documentation for SingleCellExperiment methods, where aggregateCellsToSamples is called internally. This was propagating to other packages where SingleCellExperiment methods are not defined, making the documentation confusing.

acidplots 0.2.22 (2020-01-20)

Minor changes:

• Updated bioverbs dependency to renamed AcidGenerics package.

acidplots 0.2.21 (2019-12-13)

Minor changes:

• plotHeatmap: Increased the default break range from -2:2 up to -3:3. This helps improve the dynamic range a bit for some RNA-seq plots.

acidplots 0.2.20 (2019-12-09)

Minor changes:

• Hardened user-defined interestingGroups input against NA values causing values to drop in plots. This was discovered with plotPCA calling geom_point internally, which caused removal of rows. If we coerce NA value to "NA" first, then removal no longer occurs. This is accomplished internally using str_remove_na (see also stringi_remove_na). The change applies to these functions: plotCellCounts, plotCounts, plotCountsPerBiotype, plotCountsPerBroadClass, plotCountsPerFeature, plotFeaturesDetected, plotPCA, plotTotalCounts, plotZerosVsDepth.

acidplots 0.2.19 (2019-11-19)

Minor changes:

• plotCounts: The gene argument is now optional, supporting subset SummarizedExperiment objects. Currently a maximum of 20 genes (rows) are allowed to pass through in the method.
• Updated documentation to support roxygen2 7.0 release.
• Improved default color palettes for plotHeatmap, plotCorrelationHeatmap, and plotQuantileHeatmap.

acidplots 0.2.18 (2019-11-12)

Minor changes:

• plotCounts: Reworked medianLine argument and renamed to simply line. Now supports mean and geometric mean in addition to median now. Line is now disabled by default.

acidplots 0.2.17 (2019-11-07)

Minor changes:

• Updated dependencies to require Bioconductor 3.10 release.
• Added return value for matchLabels in documentation.

acidplots 0.2.16 (2019-09-17)

Major changes:

• Replaced title argument with labels argument for functions that render plots using ggplot2.
• Now exporting matchLabels function, that handles internal ggplot2 label matching, and auto-populates with defaults in formal argument.
• Using "samplesAxis" and "countsAxis" labels for ggplot2 return that support multiple geoms. Consider a similar approach for QC metric plots.

Minor changes:

• Simplified internal handoff from SingleCellExperiment S4 methods to SummarizedExperiment, using standard ... passthrough instead of relying upon matchArgsToDoCall.
• Improved color palette consistency in plotting functions.
• plotCounts: Moved DESeqDataSet method to DESeqAnalysis package.

acidplots 0.2.15 (2019-09-13)

Major changes:

• acid_theme_dracula: New dark mode theme supporting Dracula color palette.
• Exporting color palette vectors: lightPalette, darkPalette, draculaPalette, iOSLightPalette, iOSDarkPalette, macOSLightPalette, macOSDarkPalette.
• synesthesia: Simplified color palette to use purple, blue, green, orange. User can tweak the palette using a new palette argument.

acidplots 0.2.14 (2019-08-27)

Minor changes:

• plotCountsPerFeature: Renamed formals to match conventions in new basejump melt methods.
• Updated basejump dependencies and NAMESPACE.
• Tightened up if/then checks, ensuring boolean flag return.
• Improved some working examples and unit tests.

acidplots 0.2.13 (2019-08-21)

Minor changes:

• plotPCA: Improved automatic ntop argument handling when passing in a value greater than the number or features (rows) defined in the object.
• Improved documentation for SingleCellExperiment methods that need to average or aggregate expression at sample level.
• Removed dplyr and magrittr dependencies.

acidplots 0.2.12 (2019-08-20)

Minor changes:

• Improved consistency of internal tibble handling inside plot functions.
• Updated basejump dependency versions.

acidplots 0.2.11 (2019-08-12)

Major changes:

• Migrated some QC plotting functions previously defined in bcbioSingleCell package. This makes it possible to share the code for new Chromium package, designed for importing single cell RNA-seq data from 10X Genomics.

acidplots 0.2.10 (2019-08-06)

Minor changes:

• Improved documentation consistency by importing shared parameter roxygen from the new AcidRoxygen package.
• Updated basejump dependency versions.

acidplots 0.2.9 (2019-07-30)

Minor changes:

• Updated basejump dependency versions.
• Updated some unit tests to reflect RangedSummarizedExperiment example update in AcidTest package.

acidplots 0.2.8 (2019-07-29)

Minor changes:

• Improved warning suppression for partial match in pheatmap calls.
• Improved documentation.
• Improving automatic plot title and label handling with new makeLabel and makeTitle functions from syntactic update.

acidplots 0.2.7 (2019-07-23)

New functions:

• plotCountsCorrelation and plotCountsCorrelationHeatmap: New functions optimized for plotting correlation between gene expression matrices. Particularly useful for comparing pseudoaligned vs. aligned counts, which is implemented in the new bcbioRNASeq package update.

Minor changes:

• Improved naming consistency of internal S4 functions.
• Updated basejump dependencies.

acidplots 0.2.6 (2019-07-18)

Minor changes:

• plotCountsPerBiotype: Internal tidyeval bug fix for call to dplyr::top_n. Previously, the n argument supported direct variable input, but now it must be unquoted, due to change in underlying rlang engine following the 0.4 update.

acidplots 0.2.5 (2019-07-17)

Minor changes:

• upset: Compatibility update for UpSetR v1.4 release.
• Compatibility fixes for basejump v0.10.11 release.

acidplots 0.2.4 (2019-05-08)

Minor changes:

• Improved log2 and log10 axis scale handling for plotCountsPerBiotype and plotCountsPerBroadClass. Previously, the breaks argument was defined in internal scale_y_continuous ggplot2 call, but this doesn't perform well for many RNA-seq datasets at log2 scale. Instead, it's better to log2 scale the data first and then simplify indicate log2 on the y axis title.
• plotCountsPerFeature: Improved custom color handling for density geom. Removed violin geom support but added jitter geom support. The violin plot method doesn't scale well for multiple samples, and the boxplot is visually easier to interpret for this metric, in general.

acidplots 0.2.3 (2019-05-05)

Major changes:

• Now pinned against R >= 3.5.

acidplots 0.2.2 (2019-04-26)

Major changes:

• Now importing upset function from UpSetR, with modified formals, so we can easily call this from other packages, including DESeqAnalysis.

acidplots 0.2.1 (2019-04-25)

New functions:

• New gradient palette functions: purpleOrange, blueYellow.
• Remove gplots package from imports.

Major changes:

• plotHeatmap now supports automatic color calculation when breaks argument is defined. Also improved support for legendBreaks.

Minor changes:

• Fix .pheatmapColorPalette internal check for color, which requires n argument, rather than assuming positional variable.
• plotCountsPerFeature: Improve the count subtitle.
• S4 generic reexport documentation fixes.
• Miscellaneous documentation fixes.

acidplots 0.2.0 (2019-04-22)

Reworked package, consolidating previous minimalism and firestarter packages.

New functions:

• synesthesia color palette functions.
• acid_coord_flip: Intelligently puts samples at the top of the Y axis when flipped. Particularly useful for barplots.
• acid_pretty_breaks: Attempt to improve scales::pretty_breaks, using an approach more similar to the base plot engine.
• Renamed ggplot2 themes: acid_theme_light, acid_theme_dark.

Major changes:

• All ggplot2 geoms and transformations (ggproto functions) now consistently use acid_ as a prefix.

Minor changes:

• plotCountsPerBiotype and plotCountsPerBroadClass now support title.

Deprecations:

• plotCountsPerGene has been renamed to plotCountsPerFeature.
• plotGenesDetected has been renamed to plotFeaturesDetected.
• Deprecated theme_paperwhite and theme_midnight in favor of acid_theme_light and acid_theme_dark.

acidplots 0.1.2 (2019-04-18)

New functions:

• base_breaks: An attempt as automatic pretty breaks based on the default R plotting engine. Derived from a Stack Overflow post (see documentation).

Minor changes:

• plotCountsPerBiotype, plotCountsPerBroadClass switched to recommending log10 counts by default.

acidplots 0.1.1 (2019-04-15)

Updated packages depencies and switched to Docker for Travis CI.

acidplots 0.1.0 (2019-03-28)

Initial release, migrating ggplot2 functions from basejump package.