stothard-group / cgview-js Goto Github PK

"gc-content gc-skew" has not been drawn to the maximum magnification. After completion, the sequence gap will be very large, and then it will go blank after moving it. Your demo will also have this problem.
And even if it is not maximized, after "gc-content gc-skew" is completed, the canvas will appear or be partially offset.

The documentation says：Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs
If there are 20 million data and 20,000 features, will there be any problems?
Thanks

Hi,
I am currently trying to display Single Nucleotide Polymorphisms but it doesn't seems currently possible to display features of less than 2 bp.
Furthermore, labels for 1 bp features are displayed but placed between 2 bp on the backbone, making it impossible to know which nucleotide is targeted.

Hello, I want to make the Labels font color correspond to its feature color, here is my code:

I give each label a color iteratively and print the _rgbaString property on the console to make sure it has been given a color, but why is the label font color on the page still black? Nothing has changed, please help me! Thanks!

A two-point pinch gesture zooms but the zoom position is not located at the touch site (unlike when zooming is done using the mouse pointer). This link provides a demo where pinch zooming works well.

Hi! Thanks for the amazing tool.

I'm just trying to visualize a linear structure by adding the attribute 'format': 'linear' to settings, but still render as circular. I would appreciate any help.

<!-- CG VIEWER -->
<script type="module">
    import cgview from 'https://cdn.jsdelivr.net/npm/[email protected]/+esm';

    var cgv = new CGV.Viewer('#my-viewer', {
        height: 800,
        width: 1000
    });

    json = {'cgview': {'features': [{'legend': 'Virulence',
                                        'name': 'IncX5_2, MF062700, ',
                                        'source': 'json-feature',
                                        'start': 129,
                                        'stop': 704,
                                        'type': 'CDS'}],
                          'legend': {'items': [{'decoration': 'arrow',
                                                'name': 'CDS',
                                                'swatchColor': 'rgb(111,187,111)'},
                                               {'decoration': 'arrow',
                                                'name': 'Virulence',
                                                'swatchColor': 'rgb(118,84,154)'},
                                               {'decoration': 'arrow',
                                                'name': 'BGC',
                                                'swatchColor': 'rgb(255,159,64)'},
                                               {'decoration': 'arrow',
                                                'name': 'Other',
                                                'swatchColor': 'rgb(81,160,238)'}]},
                          'sequence': {'length': 47656},
                          'settings': {'arrowHeadLength': 0.3,
                                       'backgroundColor': 'white',
                                       'format': 'linear',
                                       'showShading': 'true'},
                          'tracks': [{'dataKeys': 'json-feature',
                                      'dataMethod': 'source',
                                      'dataType': 'feature',
                                      'name': 'Features'}],
                          'version': '1.1.0'}}
    json = json.replace(/'/g, '"');

    // Load the JSON
    cgv.io.loadJSON(json);

    cgv.draw();
</script>

Bests,

Alejandra

Keep scrolling the mouse in the direction of the red arrow to zoom in, and misalignment will occur.

In addition, I would like to ask, after I modify the sequence and redraw it, how can I maintain the current zoom ratio and movement position? Can you provide some ideas? Thanks

Hello, I got the json file I wanted by modifying the cgview_builder.rb script, below is a screenshot of my json file, cog and translation information in features was added by me manually:

Now I have a problem, after the json file is loaded into cgv, it cannot recognize the new json information I added, such as cog and translation information cannot be recognized

The content of ${feature-cog} is undefined, I tried to modify the cgview.esm.js file, but I did not know where to modify it, may I ask what I should do? Thanks!

I'm getting the error SyntaxError: Cannot use import statement outside a module @ .../node_modules/cgview/dist/cgview.esm.js (9) when trying to import CGView from ESM and run the starter code shown below within a NextJS App(version 13.4.4)

code:

import CGV from 'cgview';

export const SchemaPlasmidMap = new CGV.Viewer('#my-viewer', {
  height: 500,
  width: 500,
  sequence: {
    // The length of the sequence
    length: 1000,
  },
});

Also unable to import using IIFE– created a separate ticket #9 for that as well.

After executing cgv.zoomTo (0, cgv. maxZoomFactor), Problem with scaling

Zooming in on a circular view and switching to a linear view routinely yields a blank map.

Hello,

The old CGView allowed to export genomes in SVG format which is convenient for instance to edit the map for publications. Is it possible to add this feature ?

I'm showing you a little bit now, I want to show you a little bit more so how do I change the code, or where do I change the code? Like the picture below:

I'm trying to use CGView in a NextJS(version 13.4.4) app, and getting the error d3 is not defined (at .../node_modules/cgview/dist/cgview.js (19502:7) from the following code.

import CGV from 'cgview/dist/cgview.js';

export const SchemaPlasmidMap = new CGV.Viewer('#my-viewer', {
  height: 500,
  width: 500,
  sequence: {
    // The length of the sequence
    length: 1000,
  },
});

I've confirmed that d3 was installed within the cgview node modules.

When trying to import from the ESM, I get a different error from within CGView (#10 ).