Question

Package for custom visualization of multiple sequence alignment

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tim.ivanov.92 • 0

@timivanov92-14799

Last seen 5.2 years ago

Is there a package to make custom visualization of multiple sequence alignments?

Specifically, i want to color some exons on a DNA alignment, knowing on their coordinates

MSA visualization • 1.2k views

ADD COMMENT • link updated 5.5 years ago by ulrich.bodenhofer ▴ 20 • written 5.5 years ago by tim.ivanov.92 • 0

score 1 · Answer 1 · 2018-10-24

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ulrich.bodenhofer ▴ 20

@ulrichbodenhofer-8624

Last seen 5.0 years ago

Austria

I do not know of a special R package. However, the 'msa' package's msaPrettyPrint() function provides access to all functionality of the TeXshade package via the 'furtherCode' argument. See the package vignette for a basic example (cf. p. 37). I hope that helps.

ADD COMMENT • link 5.5 years ago ulrich.bodenhofer ▴ 20

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thank you for the answer - this package looks quite all right, although i don't see in your example how can i actually access a single line in the alignment: it seems all i can do with this package is apply existing functions to regions inside an alignment, which is not quite my goal

ADD REPLY • link 5.5 years ago tim.ivanov.92 • 0