Circos > Documentation > Tutorials > Utilities > Random Links

Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.

If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.

Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.

10 — Helper Tools

1. Generating Random Link Data

script location

tools/randomlinks

script usage

> cd tools/randomlinks
> ./run
Done. Now look in data/links.txt.

To get the full manpage, use -man. 

> cd tools/randomlinks
> bin/randomlinks -man

Adjust the configuration file etc/randomlinks.conf to suit your needs.

details

The purpose of this script is largely for debugging. If you don't have any link data, you can generate some random link relationships between chrososomes sampled from a karyotype file.

Bias can be introduced into the placement of the random links through rules that associate the number of links (average and standard deviation - link copy number is sampled from a normal distribution) with a pair of regular expressions that define chromosome pairs.

For example, the following ruleset 

rule = . . 2 0
rule = chr12 chr14 10 2
rule = chr15 chr20 r5

defines three rules. Rules are evaluated in increasing order of specificity. The first rule affects all chromosomes and sets the baseline number of links between any chromosome pair to 2 (avg=2,sd=0). The next rule defines the number of links between chr12 and chr14 to be avg=10 sd=2. The last rule sets the number of links between chr15 and chr20 to be 5x the number defined by previous rules.

The configuration file (etc/randomlinks.conf) defines several rules that can get you started.

These random links are a great input to other link-related tools like bundlelinks and orderchr.

randomlinks manpage

NAME

randomlinks - generate a data file with random links between chromosomes

SYNOPSIS

  randomlinks -karyotype KARYOTYPE_FILE 
              {-chr_rx REGEX } -size AVG[,SD] [-nointra] [-nointer]

DESCRIPTION

Generate a Circos link file containing random links between chromosomes. Chromosomes are sampled from the karyotype file KARYOTYPE_FILE and optionally further filtered using the regular expression REGEX.

The number of links between any two chromosome pairs is determined by rules (see below). The size of the ends of each link is determined by the average and standard deviation values provided by -size. Links with thick ends are best drawn as ribbons.

Intrachromosomal links can be avoided using -nointra. Similiarly, interchromosomal links can be avoided using -nointer. The -nointer option is much less useful.

Link Multiplicity Rules

Given a filtered set of chromosomes (first sampled from the KARYOTYPE_FILE and then passed through the regular expression REGEX), the number of links joining any pair of chromosomes is determined by a set of rules.

Each rule contains two regular expressions, one for each of the chromosomes in the pair, and these determine which pairs of chromosomes the rule will apply to.

For example, if the regular expressions are '.' and '.' then all chromosome pairs are matched. However, if the regular expressions are '.' and 'chr10' then only pairs of chromosomes for which one contains chr10 are affected.

In addition to the regular expression selection filter, each rule contains either (a) avg/sd parameters used to generate a normally distributed random number which is used as the number of links between the selected chromosomes, or (b) a multiplier which is used to multiply the number of links as determined by a previous rule.

Optionally, rules may contain a sampling parameter which determines how frequently the rule is applied.

Rules are applied in increasing order of specificity. Thus, rules that affect the largest number of chromosome pairs are applied first, followed by rules that affect fewer pairs.

For more details about the syntax of rules, see etc/randomlinks.conf.

HISTORY

BUGS

AUTHOR

Martin Krzywinski

CONTACT

  Martin Krzywinski
  Genome Sciences Centre
  Vancouver BC Canada
  www.bcgsc.ca
  martink@bcgsc.ca