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This article mainly introduces the use of histograms in circos, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.

Histograms can be seen as a variant of line plot. Let's first take a look at an example.

The innermost circle in the picture is historgams. You can see that it consists of many columns, each of which is an area defined in file. The height of the column is determined by the value of this area. All the pillars share two directions, one facing inward and the other facing outward.

The corresponding data for this image are as follows:

You can see that the value of value is positive and negative. When both positive and negative numbers are included, all the positive columns are in one direction, and the negative columns are in the other direction. These are the default behaviors.

Let's look at an example of the most basic configuration file

R0, R1, max and min have been explained in detail in previous articles. Today, let's take a look at a few parameters that are unique to histogram.

1. Extend_bin

The interval of each bin is defined in advance in the file file, and extend_bin controls whether the adjacent bin is connected, for example, for the following data

You can see that there is a certain interval between these three intervals. By default, the corresponding bin on the graph must be discontiguous; when extend_bin = yes is set, the three bin will be connected.

The specific approach is to extend the defined interval in the file, for example, there is a gap between the first two bin, and the position of the middle point of this interval is taken as the termination position of the first bin and the starting position of the second bin, so that the two bin are connected.

Look at a case.

The two histogram in the graph are based on the same data. When extend_bin = no, draw according to the interval defined in file, you can see that the interval is not continuous; when extend_bin = yes, all bin become continuous.

The interval defined in the file file has been changed, and in general, extend_bin = yes is not recommended.

two。 Color related attribut

In histogram, there are four color-related attributes

Color

The color of the line

Fill_color

Filling color of bin

Background_color

Background color of bin

Fill_under

When fill_under = yes, background_color as the fill color of bin and fill_color as the color of the line overrides the value defined by color

Another thing you need to master is the skill of defining multiple colors. Take the most commonly used fille_color as an example, there are two main ways:

1. Set multiple conditions

The value is divided into different parts according to a certain threshold, and each part defines a different filling color through rule.

two。 Set a condition

Condition = 1 means that the rule works all the time, similar to while (1) in programming, and is always true. The value of fill_color here is defined by an expression.

According to the position of the value in the interval [- 1,1], the remap_int function maps to the [1Magin9] interval, generates an integer between 1 and 0, and then defines the color as a color in the spectral-9-div palette through the sprintf function.

The spectral-9-div palette is defined in the / etc/brewer.all.conf file

In this file, palettes of other colors are also defined, and the number in the middle represents the total number of colors in the palette, and you can choose the appropriate palette as needed.

Thank you for reading this article carefully. I hope the article "what is the use of histograms in circos" shared by the editor will be helpful to you. At the same time, I also hope you will support us and pay attention to the industry information channel. More related knowledge is waiting for you to learn!

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