plotPairsandplotPairsArchescheck and swap order of anchors.plotTranscriptsNULLlabel checking bug fix.
Version bump for Bioconductor 3.19 release.
plotHicSquarehas addedyaxisDirparameter for flipping the direction of genomic coordinates on the y-axis.
plotManhattanaccommodatesGRangesdata input. s
plotGenesappropriately handlestibbleinput forgeneHighlights.
plotIdeogramhas addedflipparameter to allow for flipping the ideogram so the end can be before/above the start.
plotManhattanpch mapping is compatible when number of data points is less than the number of levels of acolorbycolumn.
Version bump for Bioconductor 3.18 release.
paramsparsing removes non-standard chromosomes when identifying gene transcripts
colorbylogic parsing is patched.
plotPairs,plotPairsArches, andplotRangesallowNAfill.
- Removed extra page creation with
annoYaxisaxisLine = FALSE.
- Removed blank page creation with pdf() calls for all major plotting functions.
- Fixed
plotMultiSignalwidth and height parsing bug.
plotManhattany-scales can be reversed for Miami plot-style layouts.
Version bump for Bioconductor 3.17 release.
- Fixed page viewport parsing bug fixes related to R version 4.3.0 updates.
annoPixelsdetects and annotates all pixels forplotHicRectangleplots.
- yscales for
plotHicRectangleandplotHicTrianglereflect distance in Hi-C bins.
Version bump for Bioconductor 3.16 release.
- Fixed vignette links in "Introduction to plotgardener" vignette.
plotGenesand related functions will appropriately check for and handle customOrgDbs.getExonswill double-check for appropriate chromosome data to avoid incorrect plotting based on related chromosome contigs.
plotManhattanp-value data can be scaled according to a custom transformation, rather than being limited to -log10.plotRangeselements can be ordered randomly or by decreasing width before plotted row assignment.
mapColorscan appropriately map colors to a numeric vector with the same values, so long as a range is provided.
plotMultiSignalfunction can plot multiple signal track data sets in line with each other.calcSignalRangehelper function will calculate an appropriate range for multiple signal data sets.pageLayoutRowandpageLayoutColfunctions for generating row and column positions for a number of plot elements.- Gene transcripts can be highlighted by gene name or transcript name with the
parameter
transcriptHighlightsinplotTranscripts.
plotPairsArchesBezier curve height calculations were fixed for pairs with different sized anchors.
plotSignalcan now plot negative signal data alone or listed as a second file.- A
labelparameter has been added forplotSignalfor convenient labeling.
-
plotSignalrange parsing bug fixes were resolved. -
Note about double page rendering has been added to
pageGuideHide()documentation.
-
plotSignalbug fixes related to function not finding posSignal2 and negSignal2 variables with insufficient data. -
Documentation to introduction vignette has been added to explain double page rendering when using any removal function, particularly
pageGuideHide().
Version bump for Bioconductor 3.15 release.
hicTrianglesandhicRectanglescan now be annotated withannoDomainsorannoPixelsif they are flipped.
plotIdeogramcan now accept custom colors with afillparameter. Colors can be specified with a named or unnamed vector. To see which stains are being assigned which colors, look inside theideogramobject.
- ENTREZ IDs obtained from
AnnotationDbi::select()are subset just forENTREZIDcolumn when determining default gene priorities, eliminatingdplyrincompatible types error. - All plus and minus strand gene name label parsing in
plotGenesis now carried out only if there is a non-zero number of that strand's genes.
- Citation linked for
plotgardenerpublication in Bioinformatics.
plotSignalyrange parsing for negative scores now has fixed the typo on line 418 from "score2" to "score".
plotSignaldefault yrange parsing now catches the invalid 0,0 range and no longer throws a viewport related error.
readHicand functions related to the reading of .hic files now leaves the chromosome input formatted as is (e.g. "chr1" and "1"). Functions will throw an error if the input chromosome is not found in the chromosomes listed in the .hic file.
annoDomainscoordinates fixed forplotHicRectangle.- Clipping logic for
plotPairsArchesnow clips arches both on left and right side of plot. - Subsetting
plotPairslogic fixed to matchplotPairsArches.
clip.noAnchorsparameter inplotPairsArchesallows for inclusion or clipping of arches that do not have anchors in the given genomic region.plotPairsArchesnow allows for column name input to designatearchHeights.
:added back to readHic forstrawrregion parsing.plotHicSquaresubsetting fixed for off diagonal regions.
- All Hi-C functions now allow input of remote Hi-C files.
This package was previously called BentoBox.
- Version bump to 0.99.0 for Bioconductor package submission.
bb_mapColorsfunction for users to map a vector to a palette of colors.linecolorparameter inbb_plotPairs,bb_plotPairsArches, andbb_plotRangesnow accepts a single value, a vector of colors, acolorbyobject, or the value "fill".
- R version requirement changed to (R >= 4.1.0) for proper plot placement.
colorbyobject now has ascalePerRegionparameter to scale numericalcolorbydata to the range of data in a plotted genomic region.
bb_plotManhattanfillparamete now accepts a single value, a vector of colors, or acolorbyobject.
colorbyconstructor now includes optional palette specification.bb_plotPairs,bb_plotPairsArches, andbb_plotRangesfillparameter now accepts a single value, a vector of colors, or acolorbyobject.
GInteractionsassembly match checking moved before dataframe conversion.
- Data moved to
plotgardenerDatapackage. - Default genome assembly updated to "hg38".
- Streamlined parameter parsing and data reading logic.
- Added unit tests with
testthat. bb_annoDomainsfunction addition.bb_plotSignalvertical orientation.
- Added a
NEWSfile to track changes to the package.
- Updated viewport parsing for package
gridversion 4.1.0.