How to export the cell barcodes for each clone identified

[haigdjambazian]

Hi,

I have a question for this example vireoSNP_clones

I am able to generate the final figure with vireoSNP.plot.anno_heat but in my case I don't see how I can specify the clones. In the example I see 27 columns per clones adding up to 81 but in my case I have 6-7 donnors but they are not of equal size.

I want to be able to generate the figure showing the clustering between the barcodes and the snps detected.
At the moment the figure looks like the one on the left below. The 3 figures on the right are from this example vireoSNP_donors.

Thanks!

[huangyh09]

Hi,
For specify the clone id, you can use the clone_id = np.argmax(_model.ID_prob), as used in output 8. In the example, we know the ground truth clone id is in order, so we specified it manually.

Not sure what the issue is in your second point.

Yuanhua

[haigdjambazian]

Thanks!!
Are the SNPs also in order? How do I reorder them to have them showup grouped in the heatmap?

[haigdjambazian]

Thank you for the suggestion, the plot is clearer now.

[haigdjambazian]

Is there a way to sort the SNP such that they are grouped by their contribution to each clone?
Do I need to export them with vireo and then merge them and feed them back into the python workflow in the proper order? (edited)

Thanks again!

[haigdjambazian]

Related to this in the example the snp id are set this way "mtSNP_ids = ['mt_variant%d' %x for x in range(AD.shape[0])]"
What is the order of the SNPs in the plot generated? Are they in the order of the vcf?
Thanks!!