acidplots 0.2.0 (2019-04-22)
Reworked package, consolidating previous minimalism and firestarter packages.
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:
- All ggplot2 geoms and transformations (
ggproto functions) now consistently use
acid_ as a prefix.
plotCountsPerBroadClass now support
plotCountsPerGene has been renamed to
plotGenesDetected has been renamed to
theme_midnight in favor of
acidplots 0.2.1 (2019-04-25)
gradient palette functions:
- Remove gplots package from imports.
plotHeatmap now supports automatic color calculation when
breaks argument is defined. Also improved support for
.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 0.2.2 (2019-04-26)
- Now importing
upset function from UpSetR, with modified formals, so we can easily call this from other packages, including DESeqAnalysis.
acidplots 0.2.3 (2019-05-05)
- Now pinned against R >= 3.5.
acidplots 0.2.4 (2019-05-08)
- Improved log2 and log10 axis scale handling for
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 0.2.5 (2019-07-17)
upset: Compatibility update for UpSetR v1.4 release.
- Compatibility fixes for basejump v0.10.11 release.
acidplots 0.2.6 (2019-07-18)
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 0.2.7 (2019-07-23)
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.
- Improved naming consistency of internal S4 functions.
- Updated basejump dependencies.
acidplots 0.2.8 (2019-07-29)
- Improved warning suppression for partial match in
- Improved documentation.
- Improving automatic plot title and label handling with new
makeTitle functions from syntactic update.
acidplots 0.2.9 (2019-07-30)
- Updated basejump dependency versions.
- Updated some unit tests to reflect RangedSummarizedExperiment example update in AcidTest package.
acidplots 0.2.10 (2019-08-06)
- Improved documentation consistency by importing shared parameter roxygen from the new AcidRoxygen package.
- Updated basejump dependency versions.
acidplots 0.2.11 (2019-08-12)
- 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 0.2.12 (2019-08-20)
- Improved consistency of internal tibble handling inside plot functions.
- Updated basejump dependency versions.
acidplots 0.2.13 (2019-08-21)
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 0.2.14 (2019-08-27)
plotCountsPerFeature: Renamed formals to match conventions in new basejump
- Updated basejump dependencies and NAMESPACE.
- Tightened up if/then checks, ensuring boolean flag return.
- Improved some working examples and unit tests.
acidplots 0.2.15 (2019-09-13)
acid_theme_dracula: New dark mode theme supporting Dracula color palette.
- Exporting color palette vectors:
synesthesia: Simplified color palette to use purple, blue, green, orange. User can tweak the palette using a new
acidplots 0.2.16 (2019-09-17)
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.
- Simplified internal handoff from
SingleCellExperiment S4 methods to
SummarizedExperiment, using standard
... passthrough instead of relying upon
- Improved color palette consistency in plotting functions.
DESeqDataSet method to DESeqAnalysis package.
acidplots 0.2.17 (2019-11-07)
- Updated dependencies to require Bioconductor 3.10 release.
- Added return value for
matchLabels in documentation.
acidplots 0.2.18 (2019-11-12)
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 0.2.19 (2019-11-19)
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
acidplots 0.2.20 (2019-12-09)
- Hardened user-defined
interestingGroups input against
NA values causing values to drop in plots. This was discovered with
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:
acidplots 0.2.21 (2019-12-13)
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 0.2.22 (2020-01-20)
- Updated bioverbs dependency to renamed AcidGenerics package.
acidplots 0.2.23 (2020-02-22)
- 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 0.2.24 (2020-03-11)
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 0.2.25 (2020-04-13)
- Updated documentation and roxygen dependency to v7.1.0.
- Updated ggplot2 and other graphical R package dependencies.
plotHeatmap unit tests to harden against
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 0.2.26 (2020-04-21)
convertGenesToSymbols support to override automatic mapping of genes to symbols, which is enabled by default.
showRownames handling for automatic visualization of rows, which are now enabled by default for heatmaps with <= 50 features.
acidplots 0.2.27 (2020-06-10)
matchLabels now returns an empty list for a
NULL argument. This approach is used in the upcoming pointillism update, in the
acidplots 0.2.28 (2020-06-25)
plotWaterfall: Easily plot concentration curve (e.g. IC50) waterfall plots.
acidplots 0.2.29 (2020-07-09)
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 0.2.30 (2020-07-23)
- 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 0.2.31 (2020-08-05)
plotUpset: Adjusted ratio of dot matrix to main barplot, to handle complex multiple comparisons better.
acidplots 0.2.32 (2020-08-05)
- Now using cli package for improved message appearance.
acidplots 0.2.33 (2020-08-25)
plotUpset: reworked default formals to now include
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.
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.
- Updated default
fill arguments to inherit better from ggplot2 defaults: scale_colour_continuous and scale_colour_discrete. The defaults still inherit from
acid.color.discrete first but then fall back to the ggplot2 default global options
acidplots 0.2.34 (2020-08-25)
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 0.2.35 (2020-09-01)
geom argument to support additional visualization types other than dots. Can now plot boxplot, violin, or bar plot.
acidplots 0.2.36 (2020-09-02)
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.