transPlotR <img src="man/tranplotR-logo.png" align="right" height="200" width="180"/>

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There are some packages to plot gene structures, for example ggbio, ggtranscript... But there are still some limitations for them. The IGV software provides a good visualization for gene multiple isoforms. If you want to plot protein-coding or non-coding genes, it seems a little bit difficult for you to draw with a lot of codes. Here I developed a small R package named transPlotR which makes gene structure visualization much easier. You can provide a little parameters to trancriptVis to make a plot with your own GTF files.

Besides, bedVis and trackVis functions can be used to visualize bed and bigwig files with combing transcriptVis function. All these functions will let you produce a nice track plot for some Chip-seq, ATAC-seq and m6A-seq datasets.

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Installation

You can install the development version of transPlotR like so:

rCopy
# install.packages("devtools")
devtools::install_github("junjunlab/transPlotR")

Requirement

• rtracklayer, ggarchery, geomtextpath, ggnewscale, purrr

Citation

Jun Z (2022). transPlotR: An elegant package to visualize gene structures. https://github.com/junjunlab/transPlotR, https://github.com/junjunlab/transPlotR/wiki/TransPlot-documentation

Figure

More examples

• https://github.com/junjunlab/transPlotR/wiki/TransPlot-documentation
• https://github.com/junjunlab/transPlotR/wiki/TransPlot-0.0.3-documentation

Related blogs

• transPlotR 优雅的绘制基因转录本结构
• trancriptVis 的左膀右臂: bedVis 和 trackVis
• linkVis 可视化基因位点连接
• trackVis 给 track 加个背景色
• trancriptVis 可视化 NCBI 的 GTF 文件
• trackVis 在图里添加样本标签
• trackVis 给样本加个分组注释
• trackVis 居然可以自由修改 Y 轴范围
• trackVis 修改样本顺序和分组顺序