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This article introduces the relevant knowledge of "how to draw a circos diagram". Many people will encounter such a dilemma in the operation of actual cases, so let the editor lead you to learn how to deal with these situations. I hope you can read it carefully and be able to achieve something!

Data preparation

Drawing requires two basic contents, one is the chromosome information file (karyotype file), the main purpose is to display the chromosome in the picture, and color and other related settings; the other is the label text file (text text file), the main purpose is to display the gene as label in the specific position on the chromosome.

Karyotype file (chr.info)

The format is as follows:

Chr-1 Chr1 0 30427671 chr1chr-2 Chr2 0 19698289 chr2chr-3 Chr3 0 23459830 chr3chr-4 Chr4 0 18585056 chr4chr-5 Chr5 026975502 chr5

Files are separated by TAB, the first two columns can remain the same, but you need to pay attention to the information from the third column to the last column, the third column is the actual chromosome number, the fourth column is the number displayed on the picture, the fifth column indicates the beginning of the chromosome length, the sixth column corresponds to the end of the chromosome, that is, the final length, the last column actually controls the color of the chromosome, and chr1 to chr5 all correspond to different colors.

Text file (text.txt)

The file format is as follows (24 lines in all, only part of it is shown here):

5 25982254 25986435 AT5G650504 17835217 17838969 AT4G379404 12023824 12028004 AT4G229503 22618259 22620529 AT3G611201 25982294 25986349 AT1G69120

The document is still separated by TAB, the first column indicates the actual number of the chromosome on which the label text (gene) appears, the second column and the third column indicates the starting and ending coordinates of the gene on the chromosome, and the fourth column is the ID of the gene, that is, the text displayed on the chromosome.

Drawing configuration

To do circos drawing, you need to organize the configuration file according to the final goal, that is, to set various details for the image. Take the target image as an example, the configuration file (config.txt) is as follows:

Chromosomes_units=100000 # chromosomes_reverse=/ [12345] / fill=yes label_font=default label_parallel=yes label_radius=1.1r label_size=45 radius=0.5r show_label=yes default=0.005r stroke_color=dgrey stroke_thickness=2p thickness=0.03r karyotype=/share/circos/result/chr.info type=text color=red file=/share/circos/result/text.txt Label_font=condensed label_size=30 label_snuggle=yes reference: https://www..com/article/678 show_links=yes link_color=black link_dims=0p 20pmae50pmae2pmae2p link_thickness=2p r0mm 1r r1=1r+200p rpadding=5p show_tick_labels=yes show_ticks=yes color=black multiplier=1e-6 radius=1r thickness=2p size=10p spacing=5u color=black format=%d label_offset=10p label_size=25p show_label=yes size=15p spacing=10u thickness=4p

Command line drawing

After installing the software, run the drawing command to get the basic picture:

/ share/work/biosoft/circos/circos-0.69/bin/circos-conf config.txt-- outputdir. /-outputfile test "how to draw a circos diagram" ends here. Thank you for reading. If you want to know more about the industry, you can follow the website, the editor will output more high-quality practical articles for you!

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