geneviewer is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more. To explore all features visit the package website.
geneviewer is still in the development stage which might lead to breaking changes and thus not yet released on CRAN. You can install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("nvelden/geneviewer")The below example demonstrates using geneviewer to
plot a gene cluster on a genomic sequence, using the start and end
positions of each gene. The genes are grouped by class and labels are
added using the GC_labels function.
library(geneviewer)
# Data
gene_cluster <- data.frame(
name = c("ophB1", "ophC", "ophA", "ophD", "ophB2", "ophP", "ophE"),
start = c(2522, 5286, 9536, 12616, 13183, 19346, 20170),
end = c(4276, 4718, 10904, 11859, 15046, 16016, 21484),
class = c("Monooxygenase", "NTF2-like", "Methyltransferase",
"O-acyltransferase", "Monooxygenase", "Prolyloligopeptidase",
"F-box/RNHI-like")
)
# Chart
GC_chart(gene_cluster, group = "class", height = "100px") %>%
GC_labels("name")
For additional examples and the corresponding code to create the plots, please visit the Examples section.
If you encounter any issues or have feature requests, please open an Issue.