Closed Alchimic007 closed 5 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
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
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