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ViennaRNA / forgi

An RNA manipulation library.
GNU General Public License v3.0
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I can't visualize RNA with color #37

Open Shunsuke-1994 opened 4 years ago

Shunsuke-1994 commented 4 years ago

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.