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Circos plot of cis vs trans protein associations

Source: R/circos.cis.vs.trans.plot.R
circos.cis.vs.trans.plot.Rd

Visualizes cis- and trans-protein associations along chromosomes using a circular genome plot (Circos plot).

Usage

circos.cis.vs.trans.plot(f, panel, id, radius = 1e+06)

Arguments

f

Character string. Path to a tab-delimited file containing pQTL hits. Must include columns: CHR, BP, SNP, and prot.

panel

Data frame. Annotation panel containing at least: prot, uniprot, chr, start, end, and gene.

id

Character identifier passed to cis.vs.trans.classification().

radius

Numeric distance threshold defining the cis region (default: 1e6 base pairs).

Value

A Circos plot is drawn to the current graphics device. The function returns invisibly.

Details

The function classifies protein-QTL (pQTL) hits into cis and trans associations and displays genomic links between protein loci and target genes.

This version is robust to differences in column naming conventions (e.g. dot vs underscore formats).

This function relies on circlize for visualization and assumes that cis.vs.trans.classification() returns a list containing a data frame data with cis/trans annotations.

Column names may vary depending on package version. The implementation attempts flexible matching of:

  • p.chr or p_chr

  • cis.start or cis_start

  • cis.end or cis_end

  • p.gene or p_gene

  • p.prot or p_prot or prot

Examples

if (FALSE) { # \dontrun{
f <- file.path(find.package("pQTLtools"),"tests","INF1.merge")
circos.cis.vs.trans.plot(f, inf1, id = "uniprot")
} # }