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This article mainly explains "how to use circos colors". Friends who are interested might as well take a look. The method introduced in this paper is simple, fast and practical. Now let the editor take you to learn how to use circos colors.

The color attribute is the most frequently used attribute in circos, which is set by the block of colors, and the default profile is etc/circos.conf.

In circos, each color has a unique name through which the color value is called. The values of various colors are defined in the configuration file, and there are three ways to define color values

Rgb

Hsv

Lch

The above three ways correspond to three different color systems. Rgb corresponds to RGB color mode. Various colors are obtained through the superposition of R (red), G (green) and B (blue) primary colors. The value range of each primary color is 0-255 HSV corresponding to HSV color model, H represents hue, S represents saturation, V represents lightness. Lch corresponds to LCH color space, L represents luminance, C represents chromaticity, H represents hue, of which RGB model is the most widely used, as long as you master this model.

The color definition is written as follows

Red = 255j0j0pl 0

Red = rgb (255j0pl 0)

Red = hsv (0mai 1jue 1)

Red = lch (54, 105, 40)

The rgb color system is used by default, of course, the corresponding color system can also be specified through the function.

For common colors, such as red, blue, green, some columns of color gradients are defined in advance. Take red as an example, the corresponding color gradients are

Vvlred

Vlred

Lred

Red

Dred

Vdred

Vvdred

V stands for very, l for light, d for dark, vvlred for very very light red, and vvdred for very very drak red, and the whole color gradient changes from very light red to very dark red. We only need to remember the name of a few basic colors, and we can get a variety of colors with distinct layers through the vmaine prefix.

In etc/colors.conf, the following three color profiles are also introduced

Colors.brewer.conf

Colors.ucsc.conf

Colors.hsv.conf

A series of color list is defined in colos.brewer.conf in the following format

Palette-numcolors-type-idx

Palette represents the name of the color gradient; numcolors represents the number of colors contained in the color gradient; type represents the type of color gradient, seq is graded on the basis of the background color, div is more distinct, qual has a large group of colors, and idx represents the subscript, as shown below

Examples are as follows

Blues-5-seq = blues-5-seq- (\ d +)

Blues-5-seq-rev = rev (blues-5-seq- (\ d +))

Blues-5-seq-1 = 239243255

Blues-5-seq-2 = 189215231

Blues-5-seq-3 = 107174214

Blues-5-seq-4 = 49130189

Blues-5-seq-5 = 8pm 81156

Blues is the name of this color gradient, 5 means there are 5 colors with this color gradient, seq represents the color type, you can see that the gradient is based on blue, so it is the seq type, 1-5 defines 5 specific colors.

Just specify the name of color list. A color list will have two color gradients of forward and reverse, such as blue-5-seq and blue-5-seq-rev. Rev means reverse. When using it, you can choose whether to reverse it according to your own situation.

Colors.ucsc.conf defines the colors of ideogram and cytoband

1. The color of the chromosome

# Default UCSC color scheme for chromosome colors.

Chr1 = 153jue 102jue 0

Chr2 = 102, 102 and 0

Chr3 = 153pm 153pm 30

Chr4 = 204j0j0pl 0

Chr5 = 255j0j0pl 0

Chr6 = 2557.0204

Chr7 = 255204204

Chr8 = 255pm 153jue 0

Chr9 = 255jue 204jue 0

Chr10 = 255pm 255pm 0

2. The corresponding color of band

# Karyotype band colors for ideograms

Gpos100 = 0pl 0c0pl 0

Gpos = 0pl 0c0pl 0

Gpos75 = 130130130

Gpos66 = 160160160

Gpos50 = 200200200

Gpos33 = 210210210

Gpos25 = 200200200

Gvar = 220220220

Gneg = 255255255

Acen = 217pr 47pl 39

Stalk = 100127164

Color.hsv.conf uses the HSV color system to define multiple colors, as shown in the following example

Hue000 = hsv (0mai 1jue 1)

Hue001 = hsv (1pm 1pm 1)

Hue002 = hsv (2, 1, 1)

Hue003 = hsv (3, 1, 1)

Hue004 = hsv (4, 1, 1)

Hue005 = hsv (5, 1, 1)

Hue006 = hsv (6, 1, 1)

Hue007 = hsv (7 and 1)

Hue008 = hsv (8, 1, 1)

Hue009 = hsv (9, 1, 1)

Hue010 = hsv (10, 1, 1)

Through the above configuration files, we can already get most of the color names. In the etc directory, there is also a colors.unix.txt file. This file saves the definitions of commonly used colors, as shown in the following example

Alice_blue = 240248255

Aliceblue = 240248255

Antique_white = 250235215

Antiquewhite = 250235215

Antiquewhite1 = 255239219

Antiquewhite2 = 238223204

The above four files cover all the color-related configurations in circos. After understanding these files, you no longer have to worry about the assignment of color attributes.

At this point, I believe you have a deeper understanding of "how to use circos colors". You might as well do it in practice. Here is the website, more related content can enter the relevant channels to inquire, follow us, continue to learn!

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