Help with online editor for other species

[annerilotter]

Hi

I love this project and the visualizations that can be created with it.

I wanted to ask if you could provide some guidance to generate a 'plain' circos for a non-reference organism using the online editor (I understand that you may not support this at the moment, but I would love if you could). I am struggling to understand how to set up the input data to generate a circus with just the chromosomes represented. What I have is as following:

Chromosome,chromStart,chromEnd,Name
Chr01,0,44965197,Chr01
Chr02,0,59529170,Chr02
Chr03,0,83952244,Chr03
Chr04,0,41160059,Chr04
Chr05,0,76243064,Chr05
Chr06,0,57472304,Chr06
Chr07,0,54830020,Chr07
Chr08,0,72515979,Chr08
Chr09,0,39307835,Chr09
Chr10,0,37777128,Chr10
Chr11,0,44836791,Chr11

When I use the URL for this data, the image does not render the new data as input. Am I maybe missing something?

Kind regards

[sehilyi]

Hi @annerilotter! Thank you for the kind word and for visiting here to ask a question. And sorry for the a bit delayed response!

The use of other species is supported by specifying the custom chromosome names and lengths using assembly. I created a spec that works with your example that you can refer to.

Spec

{
  "assembly": [
    ["Chr01", 44965197],
    ["Chr02", 59529170],
    ["Chr03", 83952244],
    ["Chr04", 41160059],
    ["Chr05", 76243064],
    ["Chr06", 57472304],
    ["Chr07", 54830020],
    ["Chr08", 72515979],
    ["Chr09", 39307835],
    ["Chr10", 37777128],
    ["Chr11", 44836791]
  ],
  "layout": "circular",
  "centerRadius": 0.6,
  "views": [
    {
      "spacing": 1,
      "tracks": [
        {
          "data": {
            "type": "csv",
            "url": "https://gist.githubusercontent.com/sehilyi/feaf4c87017ead51978353857d91711c/raw/0d8abf56cb62f2a1d56a07a49c34864f0d8ecfb6/annerilotter.csv",
            "chromosomeField": "Chromosome",
            "genomicFields": [
              "chromStart",
              "chromEnd"
            ]
          },
          "mark": "rect",
          "x": { "field": "chromStart", "type": "genomic"},
          "xe": { "field": "chromEnd", "type": "genomic"},
          "color": { "field": "Name", "type": "nominal"}
        }
      ]
    }
  ]
}

Screenshot

Link to Editor

Link

[annerilotter]

Hi Thank you so much for this, it really has made my day. I was really struggling to understand this from the documentation and guidelines (maybe I missed where this is specified or an example use case). Kind regards

…

On Wed, 21 Jun 2023, 18:39 sehilyi, ***@***.***> wrote: Hi @annerilotter <https://github.com/annerilotter>! Thank you for the kind word and for visiting here to ask a question. And sorry for the a bit delayed response! The use of other species is supported by specifying the custom chromosome names and lengths using assembly. I created a spec that works with your example that you can refer to. Spec { "assembly": [ ["Chr01", 44965197], ["Chr02", 59529170], ["Chr03", 83952244], ["Chr04", 41160059], ["Chr05", 76243064], ["Chr06", 57472304], ["Chr07", 54830020], ["Chr08", 72515979], ["Chr09", 39307835], ["Chr10", 37777128], ["Chr11", 44836791] ], "layout": "circular", "centerRadius": 0.6, "views": [ { "spacing": 1, "tracks": [ { "data": { "type": "csv", "url": "https://gist.githubusercontent.com/sehilyi/feaf4c87017ead51978353857d91711c/raw/0d8abf56cb62f2a1d56a07a49c34864f0d8ecfb6/annerilotter.csv", "chromosomeField": "Chromosome", "genomicFields": [ "chromStart", "chromEnd" ] }, "mark": "rect", "x": { "field": "chromStart", "type": "genomic"}, "xe": { "field": "chromEnd", "type": "genomic"}, "color": { "field": "Name", "type": "nominal"} } ] } ]} Screenshot [image: gosling-visualization (14)] <https://user-images.githubusercontent.com/9922882/247627137-9a182990-e1c1-4abb-807b-5851a0f3c681.png> Link to Editor Link <https://gosling.js.org/?full=false&spec=(B'assemblyPBQ0z965197T2A59529170T3A83952244T4A41160059T5A76243064T6A57472304T7A54830020T8A72515979T9A39307835-10A37777128-1z836791Vq'layoutjcircular'IO'centerRadiusD0.6I'viewsPB*(YOL'tracksPY*(YL'dataD(YL*JZ'urljhttps%3A%2F%2Fgist.githubusercontent.cU%2Fsehilyi%2Ffeaf4c87017ead51978353857d91711c%2Fraw%2F0d8abf56cb62f2a1d56a07a49c34864f0d8ecfb6%2Fannerilotter.ZHosUeFWjChrUosUe'G*'MFWsPX~'VLL)G'markjrect'G'xKX_xeK~A_colorK'NameAJnUinal')Y*)YV*)B%5D%0A)*%20%20-qQA'%2C%20B%0A*D!%20GILLH'chrUI%2CBJ'typejKD('fWDL**MgenUicO'spacingD1IPD%5BQ*%5B'ChrT-0UomV%5DBWieldXHStartAYBLZcsv'G*_JM')G'jD'q%5DIz1A44~HEnd%01~zqj_ZYXWVUTQPOMLKJIHGDBA-*_> — Reply to this email directly, view it on GitHub <#919 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVLZ2FMB3N5D7BZTGXRNGULXMMPTFANCNFSM6AAAAAAZLVS45I> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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