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daewoooo / SVbyEye

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plotAVA is keeping the coords after cutPafAlignments #4

Closed Rafaelsoler13 closed 1 year ago

Rafaelsoler13 commented 1 year ago

Hello again,

I'm trying to cut a PAF file of the human chr8 at specific coordinates and plot it using plotAVA. However, when I select the coordinates and cut the PAF file with cutPafAlignments, I try to plot it with plotAVA but it plots with the previous coordinates which are still selected. This does not happen with the plotMiro function. Can you solve this with the plotAVA function?

Thank you so much

Full Human chr8 chr8_full

Human chr8 cut with AVA chr8_cut_AVA

Human chr8 cut with Miro chr8_Miro

Rafaelsoler13 commented 1 year ago

Now plotMiro is not zooming also as plotAVA with the recent updates

daewoooo commented 1 year ago

Would be great to have an example code and input PAF so I can reproduce the error.

Rafaelsoler13 commented 1 year ago

Here it is!

chr8_test.paf.txt

daewoooo commented 1 year ago

See example code below to solve your problem: library(SVbyEye)

paf.table <- readPaf('chr8_test.paf.txt') plotMiro(paf.table = paf.table) paf.table.sub <- subsetPafAlignments(paf.table = paf.table, target.region = 'chr8:6000000-14000000') plotMiro(paf.table = paf.table.sub)

To allow subsetting of all-vs-all alignments will be implemented later.