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