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 make 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.
You can install the development version of transPlotR like so:
# install.packages("devtools")
devtools::install_github("junjunlab/transPlotR")Requirement:
- rtracklayer
- ggarchery
- geomtextpath
- ggnewscale
- purrr
This is a basic example:
library(transPlotR)
## basic example code
data(gtf)
# facet by gene
trancriptVis(gtfFile = gtf,
gene = c('Camk1g','Daw1','Oprk1'),
facetByGene = T)