NEWS.md

In PhanstielLab/BentoBox: Coordinate-Based Genomic Visualization Package for R

VERSION 1.9.5

NEW FEATURES

• plotHicSquare has added yaxisDir parameter for flipping the direction of genomic coordinates on the y-axis.

VERSION 1.9.4

BUG FIXES

• plotManhattan accommodates GRanges data input.

VERSION 1.9.3

BUG FIXES

• plotGenes appropriately handles tibble input for geneHighlights.

VERSION 1.9.1

NEW FEATURES

• plotIdeogram has added flip parameter to allow for flipping the ideogram so the end can be before/above the start.

BUG FIXES

• plotManhattan pch mapping is compatible when number of data points is less than the number of levels of a colorby column.

VERSION 1.9.0

Version bump for Bioconductor 3.18 release.

VERSION 1.7.7

BUG FIXES

• params parsing removes non-standard chromosomes when identifying gene transcripts

VERSION 1.7.6

BUG FIXES

• colorby logic parsing is patched.

VERSION 1.7.5

NEW FEATURES

• plotPairs, plotPairsArches, and plotRanges allow NA fill.

VERSION 1.7.4

BUG FIXES

• Removed extra page creation with annoYaxis axisLine = FALSE.

VERSION 1.7.3

BUG FIXES

• Removed blank page creation with pdf() calls for all major plotting functions.

VERSION 1.7.2

BUG FIXES

• Fixed plotMultiSignal width and height parsing bug.

CHANGES IN VERSION 1.7.1

NEW FEATURES

• plotManhattan y-scales can be reversed for Miami plot-style layouts.

VERSION 1.7.0

Version bump for Bioconductor 3.17 release.

CHANGES IN VERSION 1.5.3

BUG FIXES

• Fixed page viewport parsing bug fixes related to R version 4.3.0 updates.

CHANGES IN VERSION 1.5.2

BUG FIXES

• annoPixels detects and annotates all pixels for plotHicRectangle plots.

CHANGES IN VERSION 1.5.1

BUG FIXES

• yscales for plotHicRectangle and plotHicTriangle reflect distance in Hi-C bins.

VERSION 1.5.0

Version bump for Bioconductor 3.16 release.

CHANGES IN VERSION 1.3.8 AND 1.3.9

BUG FIXES

• Fixed vignette links in "Introduction to plotgardener" vignette.

CHANGES IN VERSION 1.3.7

BUG FIXES

• plotGenes and related functions will appropriately check for and handle custom OrgDbs.
• getExons will double-check for appropriate chromosome data to avoid incorrect plotting based on related chromosome contigs.

NEW FEATURES

• plotManhattan p-value data can be scaled according to a custom transformation, rather than being limited to -log10.
• plotRanges elements can be ordered randomly or by decreasing width before plotted row assignment.

CHANGES IN VERSION 1.3.6

BUG FIXES

• mapColors can appropriately map colors to a numeric vector with the same values, so long as a range is provided.

CHANGES IN VERSION 1.3.5

NEW FEATURES

• plotMultiSignal function can plot multiple signal track data sets in line with each other.
• calcSignalRange helper function will calculate an appropriate range for multiple signal data sets.
• pageLayoutRow and pageLayoutCol functions 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 transcriptHighlights in plotTranscripts.

CHANGES IN VERSION 1.3.4

BUG FIXES

• plotPairsArches Bezier curve height calculations were fixed for pairs with different sized anchors.

CHANGES IN VERSION 1.3.3

NEW FEATURES

• plotSignal can now plot negative signal data alone or listed as a second file.
• A label parameter has been added for plotSignal for convenient labeling.

CHANGES IN VERSION 1.3.2

BUG FIXES

• plotSignal range parsing bug fixes were resolved.

• Note about double page rendering has been added to pageGuideHide() documentation.

CHANGES IN VERSION 1.3.1

• plotSignal bug 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 1.3.0

Version bump for Bioconductor 3.15 release.

CHANGES IN VERSION 1.1.18

NEW FEATURES

• hicTriangles and hicRectangles can now be annotated with annoDomains or annoPixels if they are flipped.

CHANGES IN VERSION 1.1.17

NEW FEATURES

• plotIdeogram can now accept custom colors with a fill parameter. Colors can be specified with a named or unnamed vector. To see which stains are being assigned which colors, look inside the ideogram object.

CHANGES IN VERSION 1.1.16

BUG FIXES

• ENTREZ IDs obtained from AnnotationDbi::select() are subset just for ENTREZID column when determining default gene priorities, eliminating dplyr incompatible types error.
• All plus and minus strand gene name label parsing in plotGenes is now carried out only if there is a non-zero number of that strand's genes.

CHANGES IN VERSION 1.1.15

• Citation linked for plotgardener publication in Bioinformatics.

CHANGES IN VERSION 1.1.14

BUG FIXES

• plotSignal yrange parsing for negative scores now has fixed the typo on line 418 from "score2" to "score".

CHANGES IN VERSION 1.1.13

BUG FIXES

• plotSignal default yrange parsing now catches the invalid 0,0 range and no longer throws a viewport related error.

CHANGES IN VERSION 1.1.12

BUG FIXES

• readHic and 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.

CHANGES IN VERSION 1.1.11

BUG FIXES

• annoDomains coordinates fixed for plotHicRectangle.
• Clipping logic for plotPairsArches now clips arches both on left and right side of plot.
• Subsetting plotPairs logic fixed to match plotPairsArches.

NEW FEATURES

• clip.noAnchors parameter in plotPairsArches allows for inclusion or clipping of arches that do not have anchors in the given genomic region.
• plotPairsArches now allows for column name input to designate archHeights.

CHANGES IN VERSION 0.99.11

BUG FIXES

• : added back to readHic for strawr region parsing.
• plotHicSquare subsetting fixed for off diagonal regions.

NEW FEATURES

• All Hi-C functions now allow input of remote Hi-C files.

CHANGES IN VERSION 0.99.9

This package was previously called BentoBox.

CHANGES IN VERSION 0.99.0

NEW FEATURES

• Version bump to 0.99.0 for Bioconductor package submission.
• bb_mapColors function for users to map a vector to a palette of colors.
• linecolor parameter in bb_plotPairs, bb_plotPairsArches, and bb_plotRanges now accepts a single value, a vector of colors, a colorby object, or the value "fill".

CHANGES IN VERSION 0.0.0.14

BUG FIXES

• R version requirement changed to (R >= 4.1.0) for proper plot placement.

NEW FEATURES

• colorby object now has a scalePerRegion parameter to scale numerical colorby data to the range of data in a plotted genomic region.

CHANGES IN VERSION 0.0.0.13

SIGNIFICANT USER-VISIBLE CHANGES

• bb_plotManhattan fill paramete now accepts a single value, a vector of colors, or a colorby object.

CHANGES IN VERSION 0.0.0.12

SIGNIFICANT USER-VISIBLE CHANGES

• colorby constructor now includes optional palette specification.
• bb_plotPairs, bb_plotPairsArches, and bb_plotRanges fill parameter now accepts a single value, a vector of colors, or a colorby object.

BUG FIXES

• GInteractions assembly match checking moved before dataframe conversion.

CHANGES IN VERSION 0.0.0.11

SIGNIFICANT USER-VISIBLE CHANGES

• Data moved to plotgardenerData package.
• Default genome assembly updated to "hg38".

BUG FIXES

• Streamlined parameter parsing and data reading logic.

CHANGES IN VERSION 0.0.0.10

NEW FEATURES

• Added unit tests with testthat.
• bb_annoDomains function addition.
• bb_plotSignal vertical orientation.

CHANGES IN VERSION 0.0.0.9

NEW FEATURES

• Added a NEWS file to track changes to the package.

BUG FIXES

• Updated viewport parsing for package grid version 4.1.0.

PhanstielLab/BentoBox documentation built on May 11, 2024, 6:19 a.m.