Lineage specific plot trouble shooting

[Aishah86]

Dear,

We are looking into how freyja performs plotting on specific lineage (--lineages) on the visualization. We have plot our samples and the visualization display majorities of the lineages were group under "other". But if we look at the aggregate data "other" were not listed. Can you clarify what is happening, or any other config that we need to do.

Thank you

Hereby i attached aggregate data for Feb, for your reference

-AIshah-

[joshuailevy]

Hi Aishah!

Given the outputs provided, it seems you may just have a bunch of low level variants. When running demix, I'd recommend setting --eps to a small values (say, 0.00001) and for plotting you can lower the --thresh value as well. It may also be helpful to use the --config option to specify lineage groupings/colors, otherwise you can run out of lineage colors quite quickly and you end up with a lot of "Other".

Best,
Josh

[Aishah86]

Do you mean the --thresh used during freyja plot? most of our data the plotting will be for data with < 0.5 abundance. if let say we put --thresh 0.1 , does it mean that lineages with >0.1 abundance will be plotted?

[joshuailevy]

Apologies- this seems to have evaded me. Yes, exactly. Under the hood this gets implemented via the prepLineageDict() function.