NEWS
karyoploteR 1.21.0
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG-FIXES
- Fixed wrong positioning of chromosome names in some edge cases (github issue 114)
- kpAddLabels now work on zoomed in regions (github issue 112)
karyoploteR 1.10.0
NEW FEATURES
- Added new color managements functions including is.color and transparent
and improved the existing ones.
- Added new functions to color data elements based on different features:
chromosome, position, overlapping of regions...
- Improved gene and transcript plotting functions. Added functions to
automatically get gene symbols from OrgDb objects. Improved transcript
and gene positioning. Added a function to merge all transcripts of a gene
into one.
- kpPlotBigWig can now adjust the ymax value based on the global maximum,
per chromosome or taking into account only the visible region.
SIGNIFICANT USER-VISIBLE CHANGES
- It is now posible to add labels to the right-hand side of chromosomes
with kpAddLabels
- Improved documentation and vignette
- makeGenesDataFromTxDb does not need a karyoplot anymore. Changed parameter
order.
BUG-FIXES
- kpPlotGenes and kpPlotTranscripts no longer flip strands when plotting on
data.panel=2
- kpPlotRainfall does not error when a chromosome has no data
- Fixed inversion bug in plot.type=5
- It is now possible to use cex in plotKaryotype to specify chromosome name sizes
- Multiple small bug fixes
karyoploteR 1.7.17
NEW FEATURES
- Added autotrack function to automatically assign r0 and r1 values
- Added kpAddChromosomeSeparators to draw lines between chromosomes
- Added new plot types: "ideogram" to plot on the ideogram itself and "all" to plot over all data.panels and the ideogram
- Added kpPlotBigWig to plot data on BigWig files
- Added regioneR::toGRanges to plotKaryotype zoom, so it's now possible to specify a zoom region with UCSC style region definition (i.e. "chr2:232122-321123")
- Added colByChr function to assign colors to data elements depending on their chromosome
SIGNIFICANT USER-VISIBLE CHANGES
- Added internal conversion to GenomicRanges using regioneR::toGRanges to kpPlotRegions. It is now possible to directly plot the regions in a BED file, for example.
BUG FIXES
- Fixed a bug in the coordinate change function where plotting was out of place
- Fixed a bug in kpPlotCoverage where the coverage would not extend to the end of the chromosome
- Several minor bug fixes
karyoploteR 1.7.9
SIGNIFICANT USER-VISIBLE CHANGES
- New parameter in kpPlotMarkers to allow labels to move beyond the
chromosome limits when repositioning to avoid label overlaps
BUG FIXES
- Fixed a bug in the coordinate change function where plotting was out of place
or even invisible if the zoom object had addition seqlevels
karyoploteR 1.7.4
SIGNIFICANT USER-VISIBLE CHANGES
- The zoom region in plotKaryotype can be specified in any format accepted
by regioneR::toGRanges, including UCSC/IGV style "chr9:23000-40000".
karyoploteR 1.7.3
NEW FEATURES
- Added 'kpPlotBAMCoverage' to plot the exact coverage from a BAM file
SIGNIFICANT USER-VISIBLE CHANGES
- Improved performance of kpPlotBAMDensity. Specially in zoomed plots.
BUG FIXES
- kpAxis: Axis were not visible in zoomed plots. They are now visible.
karyoploteR 1.7.1
NEW FEATURES
- Added 'kpPlotBigWig' to plot data in bigwig files, usually data derived from BAM coverage for ChIP-seq, etc...
SIGNIFICANT USER-VISIBLE CHANGES
- Added a 'digits' parameter to 'kpAddBAseNumbers' to control the number of digits after the decimal point in genome position lables
karyoploteR 1.5.4
NEW FEATURES
- Added 'kpPlotGenes' and 'kpPlotTranscripts' to plot gene and transcript models
- Added 'kpArea' to plot shaded areas. Ideal for coverage plots, RNA-seq, ChIP-seq, etc...
SIGNIFICANT USER-VISIBLE CHANGES
- Added plot.type=4 to 'plotDefaultPlotParams'
- Added new examples and extended the tutorial at the karyoploteR tutorial and examples site at https://bernatgel.github.io/karyoploter_tutorial/
BUG FIXES
- Various minor bug fixes.
- Various documentation fixes
karyoploteR 1.3.11
NEW FEATURES
- Added zooming to create plots of regions smaller than a whole chromosome.
- Added 'kpPlotLoess' to plot a fitted loess and confidence interval for data points.
- Added 'kpPlotRainfall' to create rainfall plots from variants.
- Added 'kpPlotLinks' to plot connections between genome regions even in different chromosomes.
SIGNIFICANT USER-VISIBLE CHANGES
- New default in 'plotKaryotype': now 'plot.type' defaults to 1, a ideogram with a single data panel above it
## Other
- Added unit testing
- Created a karyoploteR tutorial and examples site at https://bernatgel.github.io/karyoploter_tutorial/
BUG FIXES
- Fixed a bug causing a misalignment between data points and plotting parameters in some edge cases.
- Various minor bug fixes.