版本变化1.10.0 - - - - - - - - - - - - - - - - - - - - - - - - - o新颜色管理功能包括添加新特性。和改进现有的颜色和透明的。o添加新功能根据不同颜色数据元素特点:染色体,位置,重叠的区域……o提高基因和转录绘图功能。添加函数自动从OrgDb获得基因符号对象。改进的成绩单和基因定位。添加一个函数来合并所有记录的基因。o kpPlotBigWig现在可以调整ymax值基于全球最大,每个染色体或只考虑地区可见。重要用户可见的变化啊,现在可能将标签添加到右边的染色体与kpAddLabels o改进的文档和装饰图案o makeGenesDataFromTxDb不需要karyoplot了。改变参数的顺序。许多o现在可以使用cex plotKaryotype指定染色体名称大小o多个小bug修复版本1.7.17变化- - - - - - - - - - - - - - - - - - - - - - - - - o自动跟踪功能,添加新特性自动分配r0和r1值o添加kpAddChromosomeSeparators区分染色体o添加新图表类型:“表意文字”情节意符本身和“所有”情节的所有数据。面板和表意文字o添加kpPlotBigWig o添加区域:情节有重大影响的数据文件:toGRanges plotKaryotype放大,所以现在可以指定一个缩放区域UCSC风格区域(即定义。 "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.