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This article is about how haploview draws a map of Manhattan. The editor thinks it is very practical, so share it with you as a reference and follow the editor to have a look.

The most common visualization method for the results of GWAS analysis is the Manhattan map. An example of a typical Manhattan chart is as follows

Each point in the figure represents a SNP locus, the Abscissa is the position of the SNP locus on the chromosome, and the ordinate is the p value calculated by association analysis. For beauty, SNP loci on different chromosomes are marked with different colors. The dotted line on the vertical axis represents the threshold, and the smaller the p value, the larger the value corresponding to the vertical axis. The SNP site above the threshold is usually considered to be associated with disease or shape.

Manhattan map is essentially a scatter chart, the drawing method is relatively simple, there are a lot of R packets can be directly out of the map, this article mainly introduces the haploview software. The software can directly read the results of the plink association analysis and then draw a Manhattan map.

The method of plink association analysis was introduced before. according to the input hapmap1.ped and hapmap1.map files, we can get an allel-level correlation analysis result, which is named as1.assoc. Haploview needs to read two files, hapmap1.map and as1.assoc.

1. Import data

After starting haploview, select the PLINK Format option, and Results File selects the result file of association analysis, which can be a file with the suffix .assoc of allel association analysis, or a file containing the suffix .model of genotype association analysis; Map file can select a file with a suffix of .map, or of course, you can select a binary map file with a suffix of .bim. After selecting, click OK.

two。 Filter data

After the import is successful, you can see the table shown below, which contains the results of the imported association analysis. The regions identified in the red box can be used to screen the results of association analysis, chromosome regions can be screened by Chr, Start Kb and End kb, and SNP loci that meet the requirements can be screened by Filter.

3. Drawing

After filtering, click the Plot button to set the parameters of the drawing. The X axis must be Chromosomes, and the Y axis usually chooses the P value. If you have corrections for multiple hypothesis tests, you can also choose the P value after correction. Scale means to deal with the value of the y-axis, there are three kinds of processing

Untransformed

-log10

Ln

In general, choose-log10. Export to SVG can export pictures in svg format.

Once set up, click OK to draw the picture. Examples are as follows

Due to the small number of SNP sites in the test data, the final effect map is not particularly beautiful.

Thank you for reading! This is the end of the article on "how to draw Manhattan by haploview". I hope the above content can be of some help to you, so that you can learn more knowledge. if you think the article is good, you can share it for more people to see!

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