Package: geneviewer 0.1.10

geneviewer: Gene Cluster Visualizations

Provides tools for plotting gene clusters and transcripts by importing data from GenBank, FASTA, and GFF files. It performs BLASTP and MUMmer alignments [Altschul et al. (1990) <doi:10.1016/S0022-2836(05)80360-2>; Delcher et al. (1999) <doi:10.1093/nar/27.11.2369>] and displays results on gene arrow maps. Extensive customization options are available, including legends, labels, annotations, scales, colors, tooltips, and more.

Authors:Niels van der Velden [aut, cre]

geneviewer_0.1.10.tar.gz
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geneviewer.pdf |geneviewer.html
geneviewer/json (API)
NEWS

# Install 'geneviewer' in R:
install.packages('geneviewer', repos = c('https://nvelden.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/nvelden/geneviewer/issues4 issues

Datasets:

On CRAN:geneviewer-0.1.10(2025-01-10)

genetics

5.82 score 36 stars 13 scripts 159 downloads 34 exports 43 dependencies

Last updated 5 hours agofrom:9d2273ec8e. Checks:5 OK, 2 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 20 2025
R-4.5-winOKJan 20 2025
R-4.5-linuxOKJan 20 2025
R-4.4-winOKJan 20 2025
R-4.4-macOKJan 20 2025
R-4.3-winERRORJan 20 2025
R-4.3-macERRORJan 20 2025

Exports:%>%gbk_features_to_dfGC_alignGC_annotationGC_chartGC_chartOutputGC_clusterGC_clusterFooterGC_clusterLabelGC_clusterTitleGC_colorGC_coordinatesGC_genesGC_gridGC_labelsGC_legendGC_linksGC_normalizeGC_scaleGC_scaleBarGC_sequenceGC_titleGC_tooltipGC_trackMouseGC_transcriptgenbank_to_fastaget_intronsmummer_alignmentprotein_blastread_bedread_fastaread_gbkread_gffrenderGC_chart

Dependencies:base64encbslibcachemclicpp11digestdplyrevaluatefansifastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimepillarpkgconfigpurrrR6rappdirsrlangrmarkdownsassstringistringrtibbletidyrtidyselecttinytexutf8vctrswithrxfunyaml

Citation

To cite package ‘geneviewer’ in publications use:

van der Velden N (2025). geneviewer: Gene Cluster Visualizations. R package version 0.1.10, https://github.com/nvelden/geneviewer.

Corresponding BibTeX entry:

  @Manual{,
    title = {geneviewer: Gene Cluster Visualizations},
    author = {Niels {van der Velden}},
    year = {2025},
    note = {R package version 0.1.10},
    url = {https://github.com/nvelden/geneviewer},
  }

Readme and manuals

geneviewer - Gene Cluster Visualizations in Rgeneviewer

geneviewer

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.

Installation

You can install the released version of geneviewer from CRAN with:

install.packages("geneviewer")

And the development version from GitHub with:

# install.packages("devtools")
# devtools::install_github("nvelden/geneviewer")
install.packages("geneviewer", repos = c('https://nvelden.r-universe.dev', 'https://cloud.r-project.org'))

Usage

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")

Examples

For additional examples and the corresponding code to create the plots, please visit the Examples section.








Issues

If you encounter any issues or have feature requests, please open an Issue.

Help Manual

Help pageTopics
BRCA1 Splice VariantsBRCA1_splice_variants
Erythromycin BlastP resultserythromycin_BlastP
Erythromycin Gene Cluster Dataerythromycin_cluster
Convert GenBank Features to Data Framegbk_features_to_df
Align gene clustersGC_align
Add Annotations to a GC_chartGC_annotation
Create a GC Chart VisualizationGC_chart
Modify Cluster SettingsGC_cluster
Add a Footer to Each Cluster in a GC ChartGC_clusterFooter
Set or Update Cluster Labels for a GC ChartGC_clusterLabel
Update cluster Title of a GC Chart ClusterGC_clusterTitle
Update Color Scheme in Gene ChartGC_color
Modify Coordinates in a GC ChartGC_coordinates
Modify Gene Characteristics within a ChartGC_genes
Update Grid Display of a GC Chart ClusterGC_grid
Add Labels to Each Cluster in a GC ChartGC_labels
Set Legend for a Gene ChartGC_legend
Add Links to GC ChartGC_links
Normalize Gene Clusters in a Genomic ChartGC_normalize
Update Scale of a GC Chart ClusterGC_scale
Update Scale Bar of a GC Chart ClusterGC_scaleBar
Update Sequence Display of a GC Chart ClusterGC_sequence
Add Title to a GC_chartGC_title
Set Tooltip for a Gene ChartGC_tooltip
Track Mouse Movement in a GC_chartGC_trackMouse
Modify Transcript Characteristics within a ChartGC_transcript
Convert GenBank to FASTA Formatgenbank_to_fasta
Shiny bindings for geneviewerGC_chartOutput geneviewer-shiny renderGC_chart
Calculate Intron Positions Based on Exonsget_introns
Human Dystrophin Transcripts Datahs_dystrophin_transcripts
Human HOX Gene Cluster Datahuman_hox_genes
Perform Sequence Alignment Using MUMmermummer_alignment
ophA Gene Cluster from Omphalotus oleariusophA_clusters
Perform Protein BLAST Analysis Within Specified Clustersprotein_blast
Read BED Filesread_bed
Read Protein Sequences from FASTA Filesread_fasta
Read Data from GenBank Filesread_gbk
Read GFF Filesread_gff