plotgardener now supports .(m)cool files for Hi-C data! Functions for
reading and extracting features from .(m)cool files include:
readCoolreadCoolBpResolutionsreadCoolNormsreadCoolChroms
.(m)cool files can now be used with any Hi-C plotting function in place of
.hic files or other data types.plotPairs and plotPairsArches check and swap order of anchors.plotTranscripts NULL label checking bug fix.Version bump for Bioconductor 3.19 release.
plotHicSquare has added yaxisDir parameter for flipping the direction
of genomic coordinates on the y-axis.plotManhattan accommodates GRanges data input.plotGenes appropriately handles tibble input for geneHighlights.plotIdeogram has added flip parameter to allow for
flipping the ideogram so the end can be before/above the start.plotManhattan pch mapping is compatible when number of data
points is less than the number of levels of a colorby column.Version bump for Bioconductor 3.18 release.
params parsing removes non-standard chromosomes when identifying gene
transcriptscolorby logic parsing is patched.plotPairs, plotPairsArches, and plotRanges allow NA fill.annoYaxis axisLine = FALSE.plotMultiSignal width and height parsing bug.plotManhattan y-scales can be reversed for Miami plot-style layouts.Version bump for Bioconductor 3.17 release.
annoPixels detects and annotates all pixels for plotHicRectangle plots.plotHicRectangle and plotHicTriangle reflect distance in
Hi-C bins.Version bump for Bioconductor 3.16 release.
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.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.mapColors can appropriately map colors to a numeric vector with the same
values, so long as a range is provided.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.transcriptHighlights in plotTranscripts.plotPairsArches Bezier curve height calculations were fixed for pairs
with different sized anchors.plotSignal can now plot negative signal data alone or listed as a second
file.label parameter has been added for plotSignal for convenient labeling.plotSignal range parsing bug fixes were resolved.
Note about double page rendering has been added to pageGuideHide()
documentation.
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 bump for Bioconductor 3.15 release.
hicTriangles and hicRectangles can now be annotated with annoDomains
or annoPixels if they are flipped.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.AnnotationDbi::select() are subset just for
ENTREZID column when determining default gene priorities, eliminating dplyr
incompatible types error.plotGenes is now
carried out only if there is a non-zero number of that strand's
genes.plotgardener publication in Bioinformatics.plotSignal yrange parsing for negative scores now has fixed the typo on
line 418 from "score2" to "score".plotSignal default yrange parsing now catches the invalid 0,0 range and no
longer throws a viewport related error.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.annoDomains coordinates fixed for plotHicRectangle.plotPairsArches now clips arches both on left and right
side of plot.plotPairs logic fixed to match plotPairsArches.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.: added back to readHic for strawr region parsing.plotHicSquare subsetting fixed for off diagonal regions.This package was previously called BentoBox.
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".colorby object now has a scalePerRegion parameter to scale numerical
colorby data to the range of data in a plotted genomic region.bb_plotManhattan fill paramete now accepts a single value,
a vector of colors, or a colorby object.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.GInteractions assembly match checking moved before dataframe
conversion.plotgardenerData package.testthat.bb_annoDomains function addition.bb_plotSignal vertical orientation.NEWS file to track changes to the package.grid version 4.1.0.