I can't visualize RNA with color #37

Shunsuke-1994 · 2020-01-20T07:03:11Z

Hi! I love forgi very much!
I am trying to visualize RNA differently colored at each nucleotide using forgi.visual.fornac module.

And, i tried this following code. But if I opend the html file, RNA is not displayed......
I'm using forgi 2.0 and python 3.7 on macOS 10.14.4

import RNA 
import forgi
import forgi.visual.mplotlib as fvm
import forgi.visual.fornac as fvf
import forgi.graph.bulge_graph as fbg


rna = "GGGUUCGCCC"
ss, _ = RNA.fold(rna) #(((....)))

nucleotide_colors = {}
for i, n in enumerate(ss):
    if n == ".":
        nucleotide_colors[i] = (255,0,0)
    else:
        nucleotide_colors[i] = (0,255,0)

color_string = fvf.nucleotide_colors_to_fornac_color_string(nucleotide_colors)
html_txt = forgi.visual.fornac.create_fornac_page_for_structure(bg, color_string)

#'\n<!DOCTYPE html>\n<meta charset="utf-8">\n\nThis is an RNA container.\n<div id=\'rna_ss\'> </div>\nThis after the RNA container.\n\n    <link rel=\'stylesheet\' type=\'text/css\' href=\'https://raw.githubusercontent.com/pkerpedjiev/fornac/master/css/fornac.css\' />\n    <script type=\'text/javascript\' src=\'https://code.jquery.com/jquery-2.1.4.min.js\'></script>\n    <script type=\'text/javascript\' src=\'https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.6/d3.min.js\'></script>\n    <script type=\'text/javascript\' src=\'https://rawgit.com/pkerpedjiev/fornac/master/js/fornac.js\'></script>\n\n    <script type=\'text/javascript\'>\n        var container = new fornac.FornaContainer("#rna_ss",\n            {\'applyForce\': true, \'allowPanningAndZooming\': true, "initialSize": [500,800], \'cssFileLocation\': "https://raw.githubusercontent.com/pkerpedjiev/fornac/master/css/fornac.css"});\n\n        var options = {\'structure\': \'(((....)))\',\n                        \'sequence\': \'NNNNNNNNNN\'};\n\n        colorStr = "0:rgb(0,255,0) 1:rgb(0,255,0) 2:rgb(0,255,0) 3:rgb(255,0,0) 4:rgb(255,0,0) 5:rgb(255,0,0) 6:rgb(255,0,0) 7:rgb(0,255,0) 8:rgb(0,255,0) 9:rgb(0,255,0) " \n\n        container.addRNA(options.structure, options);\n        cs = ColorScheme(colorStr);\n\n        container.addCustomColors(cs.colorsJson);\n        container.changeColorScheme(\'custom\'); \n    </script>\n'



with open("test_forgi_viz.txt", "w") as f:
    f.write(html_txt) 

!open test_forgi_viz.txt

Do you know what's wrong with this code? The html txt seems good, I think...
And, if you can visualize RNA colored at each nucleotide by matplotlib, please tell me how to do it.
I would appreciate if you will help me. Thank you.

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I can't visualize RNA with color #37

I can't visualize RNA with color #37

Shunsuke-1994 commented Jan 20, 2020

I can't visualize RNA with color #37

I can't visualize RNA with color #37

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Shunsuke-1994 commented Jan 20, 2020