locuszoomr0.3.8 package

Gene Locus Plot with Gene Annotations

eqtl_plot

Locus eQTL plot

genetrack_ly

Gene tracks using 'plotly'

genetracks_grob

Create gene tracks grob

genetracks

Plot gene tracks

gg_addgenes

Add gene tracks to a ggplot2 plot

gg_genetracks

Plot gene tracks

gg_scatter

Locus scatter plot using ggplot2

line_plot

Locus line plot

link_eqtl

Obtain GTEx eQTL data via LDlinkR

link_LD

Obtain LD at a locus from LDlink

link_recomb

Query UCSC for Recombination data

locus_ggplot

Locus plot using ggplot2

locus_plot

Locus plot

locus_plotly

Locus plotly

locus

Create locus object for plotting

multi_layout

Layout multiple locus plots

overlay_plot

Plot overlaying eQTL and GWAS data

quick_peak

Fast peak finder in GWAS data

scatter_plot

Locus scatter plot

scatter_plotly

Locus scatter plotly

set_layers

Set up a column of multiple plots

Download source packageRead PDF manual

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>.

  • Maintainer: Myles Lewis
  • License: GPL (>= 3)
  • Last published: 2025-03-03

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