marianattestad / dot Goto Github PK

Hello,

question in title ^^'

Other plotting tools gave me multiple cancers. Dot is very very cool, so it would be even cooler if it could accomodate easily minimap2 sam file.

Just a suggestion though.

thanks!

Hi Maria,

My understanding is that one the nucmer alignments are preprocessed with DotPrep.py, the visualization tool shows the longest unique alignments (based on their cumulative length) and the "Unique: Fully Load" button loads also the short unique ones. I am right? Is there a default value for picking the longest unique ones or the online tool is just showing the top N alignments?

Thanks,
Fernando

Hi Maria,
Thank you for this useful tool!

I have two questions.

1. How is the query displayed on y-axis of the dot plot selected?
   I inputed 20 contigs aligned to the reference genome, but the dot plot y-axis only showed 13 contigs.
   When multiple contigs are aligned in the same area, will the one with the highest alignment score be displayed?

2. What is the difference between "always" and "zoom" in the grid line option?

Thank you.

Hi there!

I love this tool and its ease of use!

Would you consider including a feature so that we can export the resulting visualization so that it can be included as a high-resolution figure in publications?

Best wishes,
Sheina

Hi Maria,

I love this tool and am currently incorporating into my software!

I noticed that I can only add one annotations track:

_dot.addAnnotationData({
    key: "0",
    data: [
        {"query": "query_scf1", "query_start": 0, "query_end": 142, "name": "query_gene1", "strand": "+"},
        ...
    ]
})

or:

_dot.addAnnotationData({
    key: "0",
    data: [
        {"ref": "ref_scf1", "ref_start": 0, "ref_end": 236, "name": "ref_gene1", "strand": "+"},
        ...
    ]
})

But if I try to add both, the second command has no apparent effect.

Is this expected behaviour, a bug or am I doing something wrong?

Thanks,
MrTomRod

Hi Maria

I have a problem with Dot: sometimes, it inverts the y-axis.

Normally, Dot and nucmer/mummerplot agree:

[left: FAM19036_FAM19038; right: FAM19038_FAM19036]

But sometimes, they do not:

[left: FAM19036_FAM14217; right: FAM14217_FAM19036]

The problem is that if the y-axis is inverted, the annotation track does not match the plot any more.

There are two potential solutions for me:

1. Make Dot always agree with mummer/nucmer (preferred)
2. Tell me how to predict when Dot inverts the y-axis, so that I can invert the annotation track

Here is the relevant data so you can reproduce the issue: https://cloud.roder.casa/s/t7ByZCajS6pdw2B

I would be very glad if you could fix the issue or give me a few hints, it would safe me a lot of time.

Best, Thomas

Hi, I find the Dot tool very useful for visualizing Mummer output! Thank you for creating this tool!

Is there a way to save the output in a high quality image? Maybe I'm missing it, but it is not obvious to me how I'd do that. Thank you!

-Elias