The locuszoomr package allows users to produce
publication ready gene locus plots very similar to those produced by the
web interface ‘locuszoom’ (http://locuszoom.org), but running purely locally in R.
Plots can easily be customised, labelled and stacked.
These gene annotation plots are produced via R base graphics or ‘ggplot2’. A ‘plotly’ version can also be generated.
Bioconductor packages ensembldb and an Ensembl database
installed either as a package or obtained through Bioconductor packages
AnnotationHub are required before installation. To run the
examples in this vignette the ‘EnsDb.Hsapiens.v75’ ensembl database
package needs to be installed from Bioconductor.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ensembldb")
BiocManager::install("EnsDb.Hsapiens.v75")Install from CRAN
install.packages("locuszoomr")Install from Github
devtools::install_github("myles-lewis/locuszoomr")locuszoomr can access the LDlinkR package
to query 1000 Genomes for linkage disequilibrium (LD) across SNPs. In
order to make use of this API function you will need a personal access
token, available from the LDlink website.
We recommend that users who want to add recombination rate lines to multiple plots download the recombination rate track from UCSC and use it as described in the section Add recombination rate.
The quick example below uses a small subset (3 loci) of a GWAS dataset incorporated into the package as a demo. The dataset is from a genetic study on Systemic Lupus Erythematosus (SLE) by Bentham et al (2015). The full GWAS summary statistics can be downloaded from https://www.ebi.ac.uk/gwas/studies/GCST003156. The data format is shown below.
library(locuszoomr)
data(SLE_gwas_sub) ## limited subset of data from SLE GWAS
head(SLE_gwas_sub)
## chrom pos rsid other_allele effect_allele p
## 1 2 191794580 rs193239665 A T 0.000723856
## 2 2 191794978 rs72907256 C T 0.000481744
## 3 2 191795546 rs6434429 C G 0.156723000
## 4 2 191795869 rs148265823 A G 0.606197000
## 5 2 191799600 rs60202309 T G 0.100580000
## 6 2 191800180 rs114544034 T C 0.022496800
## beta se OR OR_lower OR_upper r2
## 1 0.32930375 0.09741618 1.39 1.1483981 1.6824305 0.037
## 2 0.39877612 0.11423935 1.49 1.1910878 1.8639264 0.034
## 3 -0.09431068 0.06659515 0.91 0.7986462 1.0368796 0.004
## 4 -0.04082199 0.07918766 0.96 0.8219877 1.1211846 0.004
## 5 0.07696104 0.04686893 1.08 0.9852084 1.1839119 0.001
## 6 -0.16251893 0.07122170 0.85 0.7392542 0.9773364 0.019We plot a locus from this dataset by extracting a subset of the data
using the locus() function. Make sure you load the correct
Ensembl database.
if (require(EnsDb.Hsapiens.v75)) {
loc <- locus(data = SLE_gwas_sub, gene = 'UBE2L3', flank = 1e5,
ens_db = "EnsDb.Hsapiens.v75")
summary(loc)
locus_plot(loc)
}
## Gene UBE2L3
## Chromosome 22, position 21,803,736 to 22,078,323
## 514 SNPs/datapoints
## 19 gene transcripts
## 8 protein_coding, 3 snoRNA, 2 lincRNA, 2 miRNA, 2 misc_RNA, 1 pseudogene, 1 sense_intronic
## Ensembl version: 75
## Organism: Homo sapiens
## Genome build: GRCh37