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DyogenIBENS / Agora

Algorithm For Gene Order Reconstruction in Ancestors
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drawKaryotype trouble #31

Closed Alchimic007 closed 6 months ago

Alchimic007 commented 6 months ago

Hello, Firstly, thank you for such great software as AGORA. I am really sorry to disturb you, but I have met issues in reconstructed blocks visualization with misc.compareGenomes in recent tests. I have tried to visualize ancestor on human chromosomes without filtering by min size of the block (-minChrSize) and got karyograms where some block were painted black. I just want to know what black color means because in visualization of reference chromosomes there was no black color. I will attach my results to this message. Please inform me if you need any more info Thank you.

Kind regards, Maksym

AGORA_last_res1.zip AGORA_last_res2.zip

alouis72 commented 6 months ago

Hi Maksym, thank you very much for your nice feedback on AGORA. About the karyotype visualization, as I understand, you try to plot the human chromosomes according to the color of ancestral genes in N2 CARs. As I can see, if you do not limit the ancestral CARs represented in Human (eventualy by minimum size), you should have 453 colors... In fact, if I remember, misc.compareGenome can draw less than ~40 colors. I think the white and black cells represent ancestral genes from small CARs.

(From the example in the code... Here is the plot of the A0 reference genome when minChrSize=20... As you can see, you have colored CARS, then White CARS, and Black CARs). A0.pdf

I guess it should be the same for N2. Cheers, Alex

YingChen94 commented 6 months ago

Hello Alex,

Is there a way to manually select the color? For example, Fig. 1b primates in the paper has mostly grey but some segments in purple.

Thanks! Ying