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This article mainly introduces "how to use circos ticks". In daily operation, I believe many people have doubts about how to use circos ticks. The editor consulted all kinds of materials and sorted out simple and easy-to-use operation methods. I hope it will be helpful to answer the doubts about "how to use circos ticks". Next, please follow the editor to study!

In circos, use ticks block to add tick marks. The scale is the same as our scale, and we need to have a minimum unit.

The smallest unit is defined by chromosomes_units, using the following

Chromosomes_units = 1000000

Subsequent tick marks are defined based on the smallest unit. For tick marks, there are two global parameters that control how they are displayed

Show_ticks

Show_ticks = yes indicates that tick marks are displayed

Show_tick_labels

Show_tick_labels = yes shows the label on the tick mark

For tick marks, it can be composed of several different standard ticks, which is similar to the concept of centimeters and millimeters. It can mark one tick every 5m or one tick every 10m. The tick marks of each specification are defined by the block of tick. Look at the following example

The first are two global parameters that indicate that the tick mark is displayed. Then there is the ticks module. The ticks in the figure above consists of two tick.

The relevant parameters of tick marks can be divided into two categories

Display of tick marks

Radius

Radius indicates the position shown by the tick mark, using radius = 0.8r

Spacing

Spacing specifies the interval between tick marks, such as spacing = 5u, which indicates that one tick mark is marked every 5 units

Color

The color of the tick mark, using color = grey

Thickness

The thickness of the tick mark, using thickness = 2p

Size

The length of the tick mark, using size = 5p

Display of tick mark label

Show_label

Show_label = yes indicates that the label is displayed

Lable_size

Controls the size of label text, usage label_size = 5p

Label_offset

Control the offset of label, set the interval between label and tick marks, use label_offset = 10p

Skip_first_label

Do not display the first label

Skip_last_label

Do not show the last label

Multiplier

Multiplier defines the ratio between the label and the actual scale, the formula is tick_label = tick_value * multiplier, and the actual marked label needs to be multiplied by multiplier on the original basis. Multiplier = 1 / 1U, which represents the proportion of 1:1, and the actual 5u is marked with 5.

Multiplier = 10 / 1U, which represents the proportion of 10:1, and the actual 5u is marked with 50.

Mod

Mod is used to format the way the label is displayed to make the label more beautiful. Mod stands for the meaning of taking remainder.

In the case of spacing = 0.1u, there will be a scale of 10.1,10.2 between 10M-11M. When mod = 1U is added, 10.1 is divided by 1, and the remainder is 0.1, so the label corresponding to 10.1 becomes 0.1.

Suffix

Add a suffix to label, such as suffix = Mb, so that each label will end up with Mb

Prefix

Add a front to the label, such as prefix = +, so that each label is preceded by +

Format

The display of formatting label is the same as the use of the sprintf function in the perl language

At this point, the study on "how to use circos ticks" is over. I hope to be able to solve your doubts. The collocation of theory and practice can better help you learn, go and try it! If you want to continue to learn more related knowledge, please continue to follow the website, the editor will continue to work hard to bring you more practical articles!

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