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pangenome / odgi

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
https://doi.org/10.1093/bioinformatics/btac308
MIT License
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Specify the path color #479

Open minglibio opened 1 year ago

minglibio commented 1 year ago

Hi,

When I use odgi viz to visualize the sub-graph, could I specify the color of each path by myself? Or can odgi viz output the pdf or svg format, so I can change the color by myself later?

Best, Ming

subwaystation commented 1 year ago

Hi there @minglibio,

this is currently not possible. From my understanding it should be easy to add @AndreaGuarracino?

Unfortunately, it is not possible to generate a pdf or svg output, because vectorized graphics does not scale and we would run out of RAM. vg viz can output svg but does not scale. See https://academic.oup.com/view-large/figure/363721019/btac308f4.tif part (c).

ekg commented 1 year ago

We could easily quantize into an SVG.

As for setting the color it is an easy feature to add. But we would want to take another input. The current colors are hashes of the path names.

On Mon, Mar 6, 2023, 04:38 Simon Heumos @.***> wrote:

Hi there @minglibio https://github.com/minglibio,

this is currently not possible. From my understanding this could be easy to add @AndreaGuarracino https://github.com/AndreaGuarracino?

Unfortunately, it is not possible to generate a pdf or svg output, because vectorized graphics does not scale and we would run out of RAM. For example vg viz can output svg but does not scale. See for example https://academic.oup.com/view-large/figure/363721019/btac308f4.tif part (c).

— Reply to this email directly, view it on GitHub https://github.com/pangenome/odgi/issues/479#issuecomment-1455887343, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQEN6EMS7Y5RRUOU6AULW2W5CRANCNFSM6AAAAAAVGCBWVQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

minglibio commented 1 year ago

Do you have any plan to add these features @ekg

ekg commented 1 year ago

It's not blocking our work, so I can't promise it soon. More than happy to help someone develop the patch! The code for odgi viz is self contained and this is the kind of thing that can be built up with a series of small changes.

On Fri, Mar 10, 2023, 16:09 Ming Li @.***> wrote:

Do you have any plan to add these features @ekg https://github.com/ekg

— Reply to this email directly, view it on GitHub https://github.com/pangenome/odgi/issues/479#issuecomment-1463941945, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQEKCRK2BEWZVGFD7YI3W3M73VANCNFSM6AAAAAAVGCBWVQ . You are receiving this because you were mentioned.Message ID: @.***>

yeeus commented 4 months ago

Hello developers @ekg @subwaystation ! I also have some wants. I think it's helpful to color path names to annotate some cluss information like ancestry. Additionally, svg and pdf format maybe very useful for everyone. Best wishes! :)