Mapping data onto a Circos figure requires that you identify what patterns in your data are (a) likely to be important and (b) likely to be present, and create a figure that exposes such patterns. Remember, if the pattern exists, you can’t afford to miss it. If it doesn’t exist, you can’t afford to be fooled into thinking that it’s there, or left wondering whether it’s occluded by other data.

## 1. Run circos

• -debug is used for debugging

• -cdump is used for check the parsing file.

## 2. Syntax and configure files

Configuration syntax is like:

Usefule syntax: hierarchical structure <ideogram>; all data points in all plot tracks <links> and <plots>; local data points in a given track <link> and <plot>; rules <rules> and <rule>; highlight<hightlight>.

Extermal imports

Accessing configuration valuesparameter2 = conf(parameter1) or parameter2 = conf(block1,block2,parameter1) for:

Eval

Color

Use the color name given, like red, lred, vlred, vvlred, dred, vdred, vvdred. If a pure color is need, use pred. For the transparent color, red_a1, red_a2, and to red_a5. red_a1 has a 17% tansparency and red_a5 have a 83% transparency.

## 3. Ideogram

One of the most common used ideogram is the karyotypes plot. The chromosome is marked as:

for example

The cytogenetic bands data is like:

• Choose a subset of chromosomes
• Order
• Scale
• Rotation
• Chromosome color

Also, the color could be redefined as

• Position
• Show bands

For example, add the human mitochondria chromosome.

Add the following to the file data/karyotype/karyotype.human.txt

Add “hsMT” color in the file etc/colors.ucsc.conf

## 4. Highlight

### 4.1 Data type

Data type of highlight is

for exmaple,

We can also add the highlight information into the data file, for example:

### 4.3 Parameters###

r0: inner radius of highlight

r1: outer radius of highlight

offset: an offset applied to both r0 and r1 (useful for overriding default r0,r1 values defined at lower precedence)

fill_color: color of the highlight slice

stroke_color: color of the highlight border, drawn if stroke_thickness is set

stroke_thickness: border thickness, if any, of the highlight slice

z: z-depth of the highlight, controlling the order in which highlights are drawn

ideogram: toggles the position of the highlight to be within the ideogram extent

or

### 5.3 Parameters###

radius: this is the radial position of the termination of the link; for relative values, if radius < 1 then it is defined in terms of the inner ideogram radius, otherwise it is defined in terms of the outer ideogram radius

bezier_radius: the radial position of the third control point (in addition to the two positions defined by the link coordinates) used to draw the Bezier curve; if this parameter is not defined then straight lines will be used

color: color of the link line

thickness: thickness of the link line (note that this is not stroke_thickness, since the line isn’t technically stroked)

record_limit: if this is defined, the number of records read from the file is capped; coordinate records are sampled from the start of the file; useful for debugging

In each <link>, <rules> and <rule> can be applied to special ruls. Each <rule> contains three parts: a condition, formatting statements and an optional ‘flow’ statement.

Marker the priority of rules

## 6. Histograms

Histogram, line plot, scatter plot, and heat map share the same data format

for exmaple

Another data format has multiple values

for example

• Plot histogram

For multiple values, fill_color is used to set the different colors.

• Orientation
• Rules
• Backgrounds and axes
• text

text data format is

for exmaple

apply rules