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This article mainly talks about "what are the circos chromosome skills". Interested friends may wish to have a look. The method introduced in this paper is simple, fast and practical. Let's let the editor take you to learn "what are the circos chromosome skills?"

By specifying a chromosome file, you can create a basic circle diagram in circos. In addition to this basic usage, there are many techniques. This chapter introduces the advanced techniques related to chromosomes, involving the following parameters

Chromosomes_display_default

Chromosomes

Chromosomes_reverse

Chromosomes_order

Chromosomes_breaks

Chromosomes_colors

Chromosomes_radius

Chromosomes_display_default is used to control the number of chromosomes displayed. By default, the value of this parameter is yes, which shows all the chromosomes in the chromosome file. When we want to filter the chromosomes, such as showing only a portion of the chromosomes, we need to use this parameter in conjunction with the chromosomes parameter. Examples are as follows:

Chromosomes_display_default = no

Chromosomes = hs1;hs2;hs3;hs4;hs5

The chromosomes parameter specifies the name of the chromosomes to be displayed, separated by semicolons. In the above example, only 5 chromosomes in total 1-5 are displayed on the circle diagram.

The chromosomes_reverse parameter specifies chromosome inversion, and by default, all stains are arranged in the same direction (clockwise or counterclockwise, depending on the value of the angle_orientation parameter). You can use this parameter when you want to reverse the specified chromosome, as shown in the following example

Chromosomes_reverse = hs2;hs3

Look at the diagram below, all the chromosomes are arranged counterclockwise, from chr1 to chr5, the corresponding scale is also counterclockwise from small to large. After setting the chromosomes_reverse parameter, chromosomes 2 and 3 are inverted and become opposite, and the corresponding scale changes from large to small in the counterclockwise direction.

Chromosomes_order specifies the order in which chromosomes are arranged and can be used in two ways:

1. Absolute positioning method

Examples are as follows

Chromosomes = hs1;hs2;hs3;hs4;hs5

Chromosomes_order = hs2,hs3,hs1,hs5,hs4

In the absolute location method, all the chromosomes need to be specified, and the order of the chromosomes in chromosomes_order is the order of the chromosomes in the picture.

two。 Relative location method

Examples are as follows

Chromosomes_order = hs3,hs5,hs4

In the relative positioning method, you only need to specify the order of some chromosomes. In the example usage, the order of chromosomes 3-5 is specified as hs3,hs5,hs4, and only the order of these three chromosomes is adjusted. The order of chromosomes 1 and 2 remains the same, so the final order is hs1, hs2, and hs3,hs5,hs4.

Chromosomes_breaks literally means to break a chromosome, and its value is a region that is not shown in the picture and is represented by a | symbol, as shown below:

The corresponding break section in the above figure is written as follows:

Chromosomes_display_default = no

Chromosomes = hs1:0-100 × hs2lu 0-100 × hs3lt 0-100th hs4lu 0-100miths5 × hs6 × hs7 = HS8

Chromosomes_breaks =-hs1:25-75 words hs2lu 25-75 T.K.);-hs7:75-);-hs8:75-)

In chromosomes, hs1:0-100means that only the region 0100on chromosome 1 is drawn; in chromosomes_breaks,-hs1:25-75 means that the region of chromosome 25-75 on chromosome 1 is not shown as a breaks, and-hs8:75-) indicates that the whole region after chromosome 75 on chromosome 8 is used as a break.

Here the minus sign indicates the area that you do not want to display. Suppose there are chromosomes 1 to 5. If you only want to display chromosomes 1 to 3, there are two ways to write it:

Chromosomes_display_default = yes

Chromosomes =-hs4;-hs5

Chromosomes_display_default = no

Chromosomes = hs1;hs2;hs3

Chromosomes_colors represents the color of chromosomes. By default, the last column in the chromosome file represents the color of each chromosome. You can use this parameter when you want to change the color specified in the file, as shown in the following example

Chromosomes_color = hs1:red;hs2:green

Sets the color for the specified chromosomes, separated by colons between chromosomes and colors, and semicolons between multiple chromosomes. In addition to specifying chromosome name, you can also use regular expressions, as shown in the following example

Chromosomes_color = / hs/:red;/mm/:green

/ hs/ represents all chromosomes whose names contain hs characters. The above method specifies red for all chromosomes whose names contain hs and green for all chromosomes that contain mm.

Chromosomes_radius specifies the radius of the chromosome, as shown in the following example

Chromosomes_radius = hs1:0.40r;hs2:0.43r

The radius assigned to each chromosome can have the following effect:

This parameter is especially useful when we want to highlight certain chromosomes, such as the following image

Adjusting the radius corresponding to chromosome 4 to be a little smaller than other chromosomes creates a concave effect. This part of the concave area is more prominent than other areas. The practice is also simple, just adjust the value of the chromosomes_radius parameter, and the settings in the subsequent plots are the same for all chromosomes, because the R0 and R1 in plots are relative to the radius of each chromosome. In fact, in order to highlight a chromosome, you can set its radius a little larger, to create a protruding effect, will be more eye-catching.

Finally, a special writing method is introduced, and the examples are as follows

Chromosomes_display_default = no

Chromosomes = hs1 [a]: 1-50 th HS1 [b]: 150 -)

Chromosomes_radius = a _ r _ b _ 0.8

Hs1 [a]: 1-50 and HSA [b]: 150 -) chromosome 1 is divided into two parts, the region 1-50 is represented by the letter a, and the region after 150 is represented by the letter b, so when the relevant parameters of the chromosome are set later, an and b can be used to represent the corresponding region; an and b are equivalent to setting name for some regions on the chromosome, which facilitates the assignment of parameters.

At this point, I believe that everyone has a deeper understanding of "circos chromosome skills", might as well come to the actual operation of it! Here is the website, more related content can enter the relevant channels to inquire, follow us, continue to learn!

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