search

GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
211 stars 63 forks source link

Auto-diagonalize dotplot/synteny plots #2110

Open cmdcolin opened 3 years ago

cmdcolin commented 3 years ago

See for example image

This is a human-to-human alignment loaded as a PAF file

Mummerplot automatically diagonalizes the plot and flips backwards scaffolds to create a by-default better display of the same data image

We may be able to accomplish something similar, would require some computational tricks that probably exist in the mummer codebase

Being able to allow the user to manually flip a region, or re-order the regions, may be interesting as well

cmdcolin commented 3 years ago

carried over from https://github.com/GMOD/jbrowse-components/issues/1133

cmdcolin commented 2 years ago

some R code to diagonalize here http://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/

JeanQ2020 commented 6 months ago

@cmdcolin Thanks for your suggestions and sharing the R code link. I tried the R code above. Unfortunately it seems not working with multiple chromosomes. Do you have code that can generate diagonal plot between genome reference of multiple chromosomes and assembled contigs of same species? Thanks!

JeanQ2020 commented 6 months ago

here's the example code for mummerplot that takes a single sequence from each reference and target and require the start and end range of that sequences

mummerplot -x "[0,275287]" -y "[0,265111]" -postscript -p mummer mummer.mums