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