Circos > Documentation > Tutorials > Utilities > Categorical Data

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

7. Visualizing Categorical Data

script location


script usage

> cd tools/categoryviewer
# use canned data
> ./makeimage
# which runs
> cat data/individuals.txt | bin/parse-category -conf etc/parse-category.conf > data/links.txt 2> data/karyotype.txt
> ../../bin/circos -conf etc/circos.conf

The input data must be tab delimited. The individuals.txt file is an example of a randomly generated set of eye color, hair color, height and sex of 1000 individuals.

The output of parse-category is the link file, sent to STDOUT (redirect with >), and the karyotype file, sent to STDERR (redirect with 2>).


This utility tool is similar to the table viewer (Tutorial 9.5 tools/tableviewer), but instead of tabular data (stored as a matrix of rows and columns), this tool generates images of categorical data which is supplied as one record per line. This utility tool is useful in analyzing survey data, relationship between multiple choice answers, and any data in which a record is associated with two or more partitioned values (partitions can be categories, codes, or intervals).

sample data set

For the example data set, I have randomly generated a putative survey responses of 1000 individuals that asked questions about sex, hair color, eye color and height. Each record corresponds to a respondent's answers.

0       female  f       red     3       green   2       165
1       female  f       blonde  0       blue    1       156
2       female  f       brown   1       grey    3       157
3       male    m       brown   1       green   2       165
4       female  f       black   2       blue    1       164
5       female  f       brown   1       green   2       158
996     male    m       red     3       grey    3       179
997     female  f       red     3       green   2       163
998     female  f       black   2       brown   0       161
999     female  f       brown   1       brown   0       160

Each responses is given in full (e.g. green) as well as a code. The codes for hair are blonde=0, brown=1, black=2 and red=3. The codes for eyes are brown=0, blue=1, green=2 and grey=3. Height is in centimeters.

The data were geneated using a probability model in which used the frequency of hair color in the population and the probabilistic relationship between hair and eye color. This is a primitive model with manufactured parameters, but serves to illustrate the benefits of Circos visualizations of categorical data.

hair and eye color

The first sample configuration file, etc/parse-category.conf, generates an image that compares hair and eye color. The start of the links are defined by column 4 (0-index). This is the column that contains the hair code (0-3). The color parameter defines the color of the segments from which the links will start.

id  = hair
col = 4
min = 0
max = 3
rx  = \d
color = orange

Link ends are defined by the eye color code, found in column 6. Eye color segments will be green.

id  = eye
col = 6
min = 0
max = 3
rx  = \d
color = green

Once the categories for the start and end of the links are defined, the data file is parsed and turned into a format that Circos can use. One set of segments will correspond to hair color, with a segment for each distinct hair color code (value found in column 4). Another set of segments will correspond to eye color. Links between them will encode the number of records with a given hair/eye color combination.

In the first example image, the color of the links is determined by the value in column 2, which contains either "m" (male) or "f" (female). The values block defines the link format values for each value in this column.

<link_coding sex>
order = 2
use   = yes
col   = 2
m = color=black_a4
f = color=black_a8

You can add more coding blocks, which are evaluated in order of the value of the order parameter. For example,

<link_coding height>
order = 1
use   = yes
col   = 7
158 = stroke_color=green,stroke_thickness=3p
159 = stroke_color=green,stroke_thickness=3p
160 = stroke_color=green,stroke_thickness=3p
161 = stroke_color=green,stroke_thickness=3p
162 = stroke_color=green,stroke_thickness=3p
168 = stroke_color=red,stroke_thickness=3p
169 = stroke_color=red,stroke_thickness=3p
170 = stroke_color=red,stroke_thickness=3p
171 = stroke_color=red,stroke_thickness=3p
172 = stroke_color=red,stroke_thickness=3p

The rules for link formatting are simple: (1) rules triggered later (based on order parameter) overwrite any formatting set by previous rules, and (2) records with the same formatting form independent ribbons. The consequence of (2) is that you can subdivide a group of records for a given start/end category value (e.g. blonde hair/blue eye) into smaller groups based on other values (e.g. blonde/blue males and females, or blonde/blue males 170cm and blonde/blue females 160cm).

ribbon order

The order of the start and end of the ribbons on each segment is controlled by the <link_order> blocks. The following ways of ordering ribbons are supported

  • by size - ribbons are placed in decreasing order of thickness (number of records)
  • by coding - ribbons are placed in alphanumeric order of the code used to determine their format characteristics through the <link_coding> blocks
  • by other end - ribbons are placed to limit the number of crossing ribbons, and this order scheme can only be used for one of the two ends
  • by radius - ribbons are placed in increasing order of the radius of their end

Ribbon order is defined in the <link_order> block and specified for the start and end of the ribbon. For example,

start = otherend
end   = size

ribbon radius

The radial position of a ribbon can be adjusted based on any column value. This is done using <radius> blocks within the <link_start> and <link_end> blocks. The radius of the ribbon is mapped onto radius min-max range (rmin-rmax) based on the value of a column (possibly remapped) and a range of acceptable values (min-max).

For example, the block

use   = yes
col   = 7
remap = int((190-int(x))/5)
min   = 0
max   = 10
rmin  = 0.7
rmax  = 0.98

will place the start of the ribbon at a radius proportional to a remapped height value. The height value is sampled from column 7 and remapped according to the remap parameter. The effect of the remap parameter as shown here is to map the height values, which range 144-189, to a range 0-9.

Just like for formatting, radial values are used to split the record set. If you have a large number of possible radial values, you will wind up with a large number of thin ribbons, since it's likely that no more than a few records will have the same radial value. It is therefore a good idea to bin adjacent radial values together to reduce the number of ribbons and avoid having a busy, uninterpretable figure.