Package: locuszoomr 0.3.9

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:Myles Lewis [aut, cre]

locuszoomr_0.3.9.tar.gz
locuszoomr_0.3.9.zip(r-4.7)locuszoomr_0.3.9.zip(r-4.6)locuszoomr_0.3.9.zip(r-4.5)
locuszoomr_0.3.9.tgz(r-4.6-any)locuszoomr_0.3.9.tgz(r-4.5-any)
locuszoomr_0.3.9.tar.gz(r-4.7-any)locuszoomr_0.3.9.tar.gz(r-4.6-any)
locuszoomr_0.3.9.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

On CRAN:

7.02 score 59 stars 1 packages 119 scripts 747 downloads 21 exports 121 dependencies

Last updated from:633b51278d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	396
source / vignettes	OK	351
linux-release-x86_64	OK	432
macos-release-arm64	OK	222
macos-oldrel-arm64	OK	205
windows-devel	OK	375
windows-release	OK	334
windows-oldrel	OK	309
wasm-release	OK	256

Exports:eqtl_plot genetrack_ly genetracks genetracks_grob gg_addgenes gg_genetracks gg_scatter line_plot link_eqtl link_LD link_recomb locus locus_ggplot locus_plot locus_plotly multi_layout overlay_plot quick_peak scatter_plot scatter_plotly set_layers

Dependencies:abind AnnotationDbi AnnotationFilter askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib cachem cigarillo cli codetools cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray digest dplyr ensembldb evaluate farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gggrid ggplot2 ggrepel glue gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval LDlinkR lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig plotly png promises ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XML XVector yaml zoo

locuszoomr

Rendered fromlocuszoomr.Rmdusingknitr::rmarkdown

Last update: 2025-02-26
Started: 2021-11-17

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

Package: locuszoomr 0.3.9

locuszoomr: Gene Locus Plot with Gene Annotations

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Usage by other packages (reverse dependencies)