Package: locuszoomr 0.3.7
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_0.3.7.tar.gz
locuszoomr_0.3.7.zip(r-4.5)locuszoomr_0.3.7.zip(r-4.4)locuszoomr_0.3.5.zip(r-4.3)
locuszoomr_0.3.7.tgz(r-4.5-any)locuszoomr_0.3.7.tgz(r-4.4-any)
locuszoomr_0.3.7.tar.gz(r-4.5-noble)locuszoomr_0.3.7.tar.gz(r-4.4-noble)
locuszoomr_0.3.7.tgz(r-4.4-emscripten)locuszoomr_0.3.7.tgz(r-4.3-emscripten)
locuszoomr.pdf |locuszoomr.html✨
locuszoomr/json (API)
NEWS
| # 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
- SLE_gwas_sub - SLE GWAS data subset
Last updated 9 days agofrom:0c3a9213a9. Checks:6 OK, 1 FAILURE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 10 2025 |
| R-4.5-win | OK | Feb 10 2025 |
| R-4.5-mac | OK | Feb 10 2025 |
| R-4.5-linux | OK | Feb 10 2025 |
| R-4.4-win | OK | Feb 10 2025 |
| R-4.4-mac | OK | Feb 10 2025 |
| R-4.3-win | OUTDATED | Dec 29 2024 |
Exports:eqtl_plotgenetrack_lygenetracksgenetracks_grobgg_addgenesgg_genetracksgg_scatterline_plotlink_eqtllink_LDlink_recomblocuslocus_ggplotlocus_plotlocus_plotlymulti_layoutoverlay_plotquick_peakscatter_plotscatter_plotlyset_layers
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibcachemclicodetoolscolorspacecowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdplyrensembldbevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgggridggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevalLDlinkRlifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotlypngpromisesProtGenericspurrrR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Locus eQTL plot | eqtl_plot |
| 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 |
| Fast peak finder in GWAS data | quick_peak |
| 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 |
