Example GWAS data | Navigation | Add recombination rate | Add LD via LDlink | Overlay eQTL data via LDlink | Dual GWAS browsing | Saving plots | Citation | References
Package: locuszoomr 1.2.0
locuszoomr: Gene Locus Plot with Gene Annotations
Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Authors:
locuszoomr_1.2.0.tar.gz
locuszoomr_1.2.0.zip(r-4.7-x86_64)locuszoomr_1.2.0.zip(r-4.7-arm64)locuszoomr_1.2.0.zip(r-4.6-x86_64)locuszoomr_1.2.0.zip(r-4.6-arm64)locuszoomr_1.2.0.zip(r-4.5-x86_64)
locuszoomr_1.2.0.tgz(r-4.6-x86_64)locuszoomr_1.2.0.tgz(r-4.6-arm64)locuszoomr_1.2.0.tgz(r-4.5-x86_64)locuszoomr_1.2.0.tgz(r-4.5-arm64)
locuszoomr_1.2.0.tar.gz(r-4.7-arm64)locuszoomr_1.2.0.tar.gz(r-4.7-x86_64)locuszoomr_1.2.0.tar.gz(r-4.6-arm64)locuszoomr_1.2.0.tar.gz(r-4.6-x86_64)
locuszoomr_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
locuszoomr/json (API)
| # Install 'locuszoomr' in R: |
| install.packages('locuszoomr', repos = c('https://myles-lewis.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/myles-lewis/locuszoomr/issues
Datasets:
- SLE_gwas_sub - SLE GWAS data subset
Last updated from:fdf18c7187. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 314 | ||
| linux-devel-x86_64 | OK | 457 | ||
| source / vignettes | OK | 424 | ||
| linux-release-arm64 | OK | 307 | ||
| linux-release-x86_64 | OK | 378 | ||
| macos-release-arm64 | OK | 254 | ||
| macos-release-x86_64 | OK | 652 | ||
| macos-oldrel-arm64 | OK | 287 | ||
| macos-oldrel-x86_64 | OK | 636 | ||
| windows-devel-arm64 | OK | 580 | ||
| windows-devel-x86_64 | OK | 361 | ||
| windows-release-arm64 | OK | 390 | ||
| windows-release-x86_64 | OK | 346 | ||
| windows-oldrel-x86_64 | OK | 326 | ||
| wasm-release | OK | 209 |
Exports:eqtl_plotgenetrack_lygenetracksgenetracks_grobgg_addgenesgg_genetracksgg_scatterline_plotlink_eqtllink_LDlink_recomblocuslocus_ggplotlocus_plotlocus_plotlymulti_layoutoverlay_plotquick_peaksanity_checkscatter_plotscatter_plotlyset_layerszoom
Dependencies:AnnotationDbiAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibcachemcigarilloclicodetoolscommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdigestdplyrensembldbevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgggridggplot2gluegtablegtoolshighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlazyevalLDlinkRlifecyclemagrittrmemoisemimeopensslotelpillarpkgconfigplotlypngpromisesProtGenericspurrrR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4VectorsS7sassscalesSeqinfoshinysnowsourcetoolsstringistringrsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryaml
Zoom browser
Last update: 2026-10-09
Started: 2026-09-02
locuszoomr
Introduction | Installation | Example locus plot | Accessing Ensembl databases | Controlling the locus | Obtaining LD information | Add recombination rate | Customise plots and labels | Point shapes | Customise gene tracks | Plot gene annotation only | Add eQTL data via LDlink | Change y-axis variable | Arrange multiple locus plots | Layering plots | Column of plots | Overlaid plots | Add custom legend / features | ggplot2 version | Shapes | Arrange multiple ggplots | Plotly version | Plot all GWAS peaks | Manhattan & other plots | Citation | References
Last update: 2026-10-05
Started: 2021-11-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Locus eQTL plot | eqtl_plot |
| Locus eQTL scatter plotly | eqtl_plotly |
| Gene tracks using 'plotly' | genetrack_ly |
| Plot gene tracks | genetracks |
| Create gene tracks grob | genetracks_grob |
| Add gene tracks to a ggplot2 plot | gg_addgenes |
| Plot gene tracks | gg_genetracks |
| Locus scatter plot using ggplot2 | gg_scatter |
| Locus line plot | line_plot |
| Obtain GTEx eQTL data via LDlinkR | link_eqtl |
| Obtain LD at a locus from LDlink | link_LD |
| Query UCSC for Recombination data | link_recomb |
| Create locus object for plotting | locus |
| Locus plot using ggplot2 | locus_ggplot |
| Locus plot | locus_plot |
| Locus plotly | locus_plotly |
| Layout multiple locus plots | multi_layout |
| Plot overlaying eQTL and GWAS data | overlay_plot |
| Plot overlaying eQTL and GWAS data using plotly | overlay_plotly |
| Fast peak finder in GWAS data | quick_peak |
| Sanity checks on GWAS dataframes | sanity_check |
| Locus scatter plot | scatter_plot |
| Locus scatter plotly | scatter_plotly |
| Set up a column of multiple plots | set_layers |
| SLE GWAS data subset | SLE_gwas_sub |
| Zoom browser to explore GWAS/eQTL results | zoom |