How to plot figure?
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6 months ago
devarora ▴ 430

While going through a research article I found a self explanatory figure and willing to perform similar task. We have done some work and want to map certain identified genes. I am interested in research article figure 4 or 5. Please provide some lead how can I achieve my goal in this regards.

Regards Devender

enter image description here

Fst vcf wgs plot • 360 views
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Do you actually have any data yet? Otherwise the lead would be to download the data from the authors of the paper and follow the described methods (and if you run into a specific software problem, return here with a description of the problem and the data).

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Yes, I have the data and able to generate part (a). I Would like to ananlyze how they plotted part (b) and mapped all the breeds with the selected region. In this regard, any lead would be a great help or any tool that can plot such diversify information.

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The bottom part is just a heatmap - check the methods to see what it says. Then, the entire figure panels are likely pieced together manually

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6 months ago

In the figure legend it says "Haplotype diversity at the HCRTR1 (b) and SLC40A1 (d) gene regions (gray area). The major allele at each SNP position in N’Dama is colored in red, the minor one in white."

I would therefore assume that the authors had a matrix with two values, one value representing the major allele and the other one representing the minor allele. I would also guess that in that matrix columns represented individual base pairs (or genomic bins of a certain size) and rows represented individual samples. That table of values was then plotted as a heatmap. This can be done in R using various functions, e.g. pheatmap (here's a nice tutorial) or ComplexHeatmap

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I am also assuming they extracted certain coordinates and made this heatmap. I will try this with our data and if have any positive development will post the same. Thankyou so much.

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I tried to see the identified regions for haplotype distribution and able to plot a kind of similar results Figure 3 (b) research article. Thank you again for the help and support.

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