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Circos is mainly used to display the relevant data on the chromosome and visualize it in different ways according to the position on the staining.

First of all, we need a chromosome location file. In circos, the location of chromosomes is stored in a file, which is set by the karyotype parameter, such as

The location of the chromosome is saved in the file karyotype.human.txt, some of which are as follows:

Separated by\ t, a total of 7 columns of content. The first two columns are specified, both are chr, indicating that this part defines chromosome-related information, the third column is the ID of the chromosome, and the ID must be unique, used to distinguish different chromosomes, and the fourth column represents the name of the chromosome, which will be displayed in the final picture. The fifth and sixth columns represent the starting position and the ending position, respectively, where the length is the total length of the chromosome, and the last column represents the color of the chromosome, but the chr prefix is used to indicate the color, so be careful not to be confused with the ID and name of the chromosome.

In circos, there are many colors built in, and the relevant configurations are saved in the etc/colors.conf file of the software installation directory, in which the etc/colors.ucsc.conf file uses the RGB standard and defines various color values of chr.

You can also see how the color is defined by the contents of the last column in the file `karyotype.human.txt`` above.

The basic parameters of chromosomes are defined in ideogram. All parameters can be divided into the following three categories

The position of the chromosome

The color of the chromosome

The label of a chromosome

The position of the chromosome

Circos provides a circular overall layout for displaying the data of chromosomes, each of which can be seen as an arc on the circle. The position of the chromosome is defined by the distance from the chromosome to the center of the circle. Specifically, it is defined by the radius parameter.

In circos, there are two ways to define the value of this parameter

Absolute value definition

The absolute value is defined by pixels, and the corresponding suffix is p, which represents pixels. For example, radius = 1000p

Relative value definition

The relative value is suffixed with r, which means relative. In the etc/image.generic.conf file, the referenced radius is defined

Radius of inscribed circle in image

Radius = 1500p

So the radius we defined in the configuration file is 0.80r, which is actually equal to 0.8 * 1500 = 1200 pixels.

The distance between chromosomes is defined by the block of spacing, and the default parameter sets the default distance between all chromosomes.

If you want to change the distance between two chromosomes, you can use the block pairwise, which is used as follows

The specific two chromosomes are specified by the ID of the chromosome, separated by, and then the distance between them is defined by the spacing parameter.

It is important to note that the relative value is defined here. The 20r in the above example represents a distance of 20 times the relative default, so it is important to understand which relative reference is when using the relative value.

The color of the chromosome

The width of the chromosome is defined by thickness, the unit is similar to radius, there are r and p, usually we use p, it is more convenient. For example, thickness = 20p.

There are two ways to display chromosomes

Line segment mode

This mode is the default mode. In this mode, the chromosome is treated as a line, and the color is the last column in the karyotype.

Rectangular mode

In this mode, each chromosome is treated as a rectangle that can be filled, so it is made up of a border and a filling part.

Stroke_thickness and stroke_color define the width and color of the border. If you want to have a fill color, you need to set fill=yes, and the rectangle will be filled with the color defined in the last column in karyotype.

The label of a chromosome

In karyotype, we define the name of the chromosome, also known as label, and we have a series of parameters corresponding to label, so adjust its display.

By default, this name does not appear on the diagram; it can be displayed through show_label, such as show_label = yes.

Label is displayed on the picture in the form of text, label_font sets the font, label_radius sets the position, label_size sets the size, label_parallel sets the direction of label, yes represents parallel to the chromosome direction, and no represents perpendicular to the chromosome direction.

A complete example of ideogram is as follows:

Thank you for reading! This is the end of this article on "sample Analysis of deogram in circos". I hope the above content can be of some help to you, so that you can learn more knowledge. if you think the article is good, you can share it for more people to see!

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