Specifying metadata’s colors

The user can provide a dictionnary of colors for metadata.

{'nodes': [[186.00442266, 120.5, 197.00442266, 131.5, 14, None], [231.63428059999998, 135.5, 242.63428059999998, 146.5, 16, None], [193.18223842, 219.25, 204.18223842, 230.25, 19, None], [279.12449228, 195.5, 290.12449228, 206.5, 22, None], [247.859896, 258.0, 258.859896, 269.0, 25, None], [299.81184917999997, 235.5, 310.81184917999997, 246.5, 26, None], [305.41676496, 280.5, 316.41676496, 291.5, 29, None], [348.77341394, 295.5, 359.77341394, 306.5, 31, None], [191.02678506, 504.25, 202.02678506, 515.25, 45, None], [243.52602504, 473.0, 254.52602504, 484.0, 46, None], [376.25678880000004, 435.5, 387.25678880000004, 446.5, 48, None], [341.37313114000005, 615.5, 352.37313114000005, 626.5, 62, None], [287.43484814, 680.1875, 298.43484814, 691.1875, 67, None], [326.41151304, 655.5, 337.41151304, 666.5, 68, None], [353.65421458, 704.875, 364.65421458, 715.875, 71, None], [633.01872738, 724.25, 644.01872738, 735.25, 73, None], [729.50095158, 743.0, 740.50095158, 754.0, 75, None], [799.0341836, 760.5, 810.0341836, 771.5, 77, None], [924.36536776, 775.5, 935.36536776, 786.5, 79, None], [172.29722116000002, 1033.009765625, 183.29722116000002, 1044.009765625, 82, None], [267.2267833, 898.0, 278.2267833, 909.0, 84, None], [343.40014422, 830.5, 354.40014422, 841.5, 86, None], [423.48756544, 815.5, 434.48756544, 826.5, 87, None], [350.11588348, 890.5, 361.11588348, 901.5, 91, None], [453.93768983999996, 875.5, 464.93768983999996, 886.5, 92, None], [350.5575784, 995.5, 361.5575784, 1006.5, 102, None], [263.24983000000003, 1040.5, 274.24983000000003, 1051.5, 105, None], [301.43951446000005, 1055.5, 312.43951446000005, 1066.5, 107, None], [265.5149251, 1121.14453125, 276.5149251, 1132.14453125, 110, None], [308.75455864, 1156.7890625, 319.75455864, 1167.7890625, 112, None], [435.19029316, 1286.75, 446.19029316, 1297.75, 125, None], [479.34608756, 1268.0, 490.34608756, 1279.0, 126, None], [507.76063906, 1250.5, 518.76063906, 1261.5, 127, None], [616.19600388, 1235.5, 627.19600388, 1246.5, 128, None], [159.31415976, 1519.4453125, 170.31415976, 1530.4453125, 135, None], [352.50666861999997, 1480.5, 363.50666861999997, 1491.5, 148, None], [448.23800501999995, 1435.5, 459.23800501999995, 1446.5, 150, None], [491.48270763999994, 1475.5, 502.48270763999994, 1486.5, 153, None], [509.53445245999995, 1535.5, 520.53445246, 1546.5, 157, None], [307.39555041999995, 1635.5, 318.39555041999995, 1646.5, 165, None], [293.94519002, 1695.5, 304.94519002, 1706.5, 170, None], [311.99732886, 1755.5, 322.99732886, 1766.5, 177, None]], 'faces': [[1167.9852429600003, 0.5, 1218.9852429600003, 21.5, 1, None], [1222.9852429600003, 0.5, 1273.9852429600003, 21.5, 1, None], [1302.9852429600003, 0.5, 1523.9852429600003, 21.5, 1, ''], [1167.9852429600003, 20.5, 1218.9852429600003, 41.5, 3, None], [1222.9852429600003, 20.5, 1273.9852429600003, 41.5, 3, None], [1302.9852429600003, 20.5, 1523.9852429600003, 41.5, 3, ''], [1167.9852429600003, 40.5, 1218.9852429600003, 61.5, 9, None], [1222.9852429600003, 40.5, 1273.9852429600003, 61.5, 9, None], [1302.9852429600003, 40.5, 1523.9852429600003, 61.5, 9, ''], [1167.9852429600003, 60.5, 1218.9852429600003, 81.5, 10, None], [1222.9852429600003, 60.5, 1273.9852429600003, 81.5, 10, None], [1302.9852429600003, 60.5, 1523.9852429600003, 81.5, 10, ''], [1167.9852429600005, 80.5, 1218.9852429600005, 101.5, 11, None], [1222.9852429600005, 80.5, 1273.9852429600005, 101.5, 11, None], [1302.9852429600005, 80.5, 1523.9852429600005, 101.5, 11, ''], [1167.9852429600003, 100.5, 1218.9852429600003, 121.5, 15, None], [1222.9852429600003, 100.5, 1273.9852429600003, 121.5, 15, None], [1302.9852429600003, 100.5, 1523.9852429600003, 121.5, 15, ''], [1167.9852429600003, 120.5, 1218.9852429600003, 141.5, 17, None], [1222.9852429600003, 120.5, 1273.9852429600003, 141.5, 17, None], [1302.9852429600003, 120.5, 1523.9852429600003, 141.5, 17, ''], [1167.9852429600003, 140.5, 1218.9852429600003, 161.5, 18, None], [1222.9852429600003, 140.5, 1273.9852429600003, 161.5, 18, None], [1302.9852429600003, 140.5, 1523.9852429600003, 161.5, 18, ''], [1167.9852429600003, 160.5, 1218.9852429600003, 181.5, 21, None], [1222.9852429600003, 160.5, 1273.9852429600003, 181.5, 21, None], [1302.9852429600003, 160.5, 1523.9852429600003, 181.5, 21, ''], [1167.9852429600003, 180.5, 1218.9852429600003, 201.5, 23, None], [1222.9852429600003, 180.5, 1273.9852429600003, 201.5, 23, None], [1302.9852429600003, 180.5, 1523.9852429600003, 201.5, 23, ''], [1167.9852429600003, 200.5, 1218.9852429600003, 221.5, 24, None], [1222.9852429600003, 200.5, 1273.9852429600003, 221.5, 24, None], [1302.9852429600003, 200.5, 1523.9852429600003, 221.5, 24, ''], [1167.9852429600003, 220.5, 1218.9852429600003, 241.5, 27, None], [1222.9852429600003, 220.5, 1273.9852429600003, 241.5, 27, None], [1302.9852429600003, 220.5, 1523.9852429600003, 241.5, 27, ''], [1167.9852429600003, 240.5, 1218.9852429600003, 261.5, 28, None], [1222.9852429600003, 240.5, 1273.9852429600003, 261.5, 28, None], [1302.9852429600003, 240.5, 1523.9852429600003, 261.5, 28, ''], [1167.9852429600003, 260.5, 1218.9852429600003, 281.5, 30, None], [1222.9852429600003, 260.5, 1273.9852429600003, 281.5, 30, None], [1302.9852429600003, 260.5, 1523.9852429600003, 281.5, 30, ''], [1167.9852429600003, 280.5, 1218.9852429600003, 301.5, 32, None], [1222.9852429600003, 280.5, 1273.9852429600003, 301.5, 32, None], [1302.9852429600003, 280.5, 1523.9852429600003, 301.5, 32, ''], [1167.9852429600003, 300.5, 1218.9852429600003, 321.5, 33, None], [1222.9852429600003, 300.5, 1273.9852429600003, 321.5, 33, None], [1302.9852429600003, 300.5, 1523.9852429600003, 321.5, 33, ''], [1167.9852429600003, 320.5, 1218.9852429600003, 341.5, 36, None], [1222.9852429600003, 320.5, 1273.9852429600003, 341.5, 36, None], [1302.9852429600003, 320.5, 1523.9852429600003, 341.5, 36, ''], [1167.9852429600003, 340.5, 1218.9852429600003, 361.5, 37, None], [1222.9852429600003, 340.5, 1273.9852429600003, 361.5, 37, None], [1302.9852429600003, 340.5, 1523.9852429600003, 361.5, 37, ''], [1167.9852429600003, 360.5, 1218.9852429600003, 381.5, 39, None], [1222.9852429600003, 360.5, 1273.9852429600003, 381.5, 39, None], [1302.9852429600003, 360.5, 1523.9852429600003, 381.5, 39, ''], [1167.9852429600003, 380.5, 1218.9852429600003, 401.5, 40, None], [1222.9852429600003, 380.5, 1273.9852429600003, 401.5, 40, None], [1302.9852429600003, 380.5, 1523.9852429600003, 401.5, 40, ''], [1167.9852429600003, 400.5, 1218.9852429600003, 421.5, 44, None], [1222.9852429600003, 400.5, 1273.9852429600003, 421.5, 44, None], [1302.9852429600003, 400.5, 1523.9852429600003, 421.5, 44, ''], [1167.9852429600003, 420.5, 1218.9852429600003, 441.5, 49, None], [1222.9852429600003, 420.5, 1273.9852429600003, 441.5, 49, None], [1302.9852429600003, 420.5, 1523.9852429600003, 441.5, 49, ''], [1167.9852429600003, 440.5, 1218.9852429600003, 461.5, 50, None], [1222.9852429600003, 440.5, 1273.9852429600003, 461.5, 50, None], [1302.9852429600003, 440.5, 1523.9852429600003, 461.5, 50, ''], [1167.9852429600003, 460.5, 1218.9852429600003, 481.5, 51, None], [1222.9852429600003, 460.5, 1273.9852429600003, 481.5, 51, None], [1302.9852429600003, 460.5, 1523.9852429600003, 481.5, 51, ''], [1167.9852429600003, 480.5, 1218.9852429600003, 501.5, 53, None], [1222.9852429600003, 480.5, 1273.9852429600003, 501.5, 53, None], [1302.9852429600003, 480.5, 1523.9852429600003, 501.5, 53, ''], [1167.9852429600003, 500.5, 1218.9852429600003, 521.5, 54, None], [1222.9852429600003, 500.5, 1273.9852429600003, 521.5, 54, None], [1302.9852429600003, 500.5, 1523.9852429600003, 521.5, 54, ''], [1167.9852429600003, 520.5, 1218.9852429600003, 541.5, 56, None], [1222.9852429600003, 520.5, 1273.9852429600003, 541.5, 56, None], [1302.9852429600003, 520.5, 1523.9852429600003, 541.5, 56, ''], [1167.9852429600003, 540.5, 1218.9852429600003, 561.5, 57, None], [1222.9852429600003, 540.5, 1273.9852429600003, 561.5, 57, None], [1302.9852429600003, 540.5, 1523.9852429600003, 561.5, 57, ''], [1167.9852429600003, 560.5, 1218.9852429600003, 581.5, 60, None], [1222.9852429600003, 560.5, 1273.9852429600003, 581.5, 60, None], [1302.9852429600003, 560.5, 1523.9852429600003, 581.5, 60, ''], [1167.9852429600003, 580.5, 1218.9852429600003, 601.5, 61, None], [1222.9852429600003, 580.5, 1273.9852429600003, 601.5, 61, None], [1302.9852429600003, 580.5, 1523.9852429600003, 601.5, 61, ''], [1167.9852429600003, 600.5, 1218.9852429600003, 621.5, 63, None], [1222.9852429600003, 600.5, 1273.9852429600003, 621.5, 63, None], [1302.9852429600003, 600.5, 1523.9852429600003, 621.5, 63, ''], [1167.9852429600003, 620.5, 1218.9852429600003, 641.5, 64, None], [1222.9852429600003, 620.5, 1273.9852429600003, 641.5, 64, None], [1302.9852429600003, 620.5, 1523.9852429600003, 641.5, 64, ''], [1167.9852429600003, 640.5, 1218.9852429600003, 661.5, 69, None], [1222.9852429600003, 640.5, 1273.9852429600003, 661.5, 69, None], [1302.9852429600003, 640.5, 1523.9852429600003, 661.5, 69, ''], [1167.9852429600003, 660.5, 1218.9852429600003, 681.5, 70, None], [1222.9852429600003, 660.5, 1273.9852429600003, 681.5, 70, None], [1302.9852429600003, 660.5, 1523.9852429600003, 681.5, 70, ''], [1167.9852429600003, 680.5, 1218.9852429600003, 701.5, 72, None], [1222.9852429600003, 680.5, 1273.9852429600003, 701.5, 72, None], [1302.9852429600003, 680.5, 1523.9852429600003, 701.5, 72, ''], [1167.9852429600003, 700.5, 1218.9852429600003, 721.5, 74, None], [1222.9852429600003, 700.5, 1273.9852429600003, 721.5, 74, None], [1302.9852429600003, 700.5, 1523.9852429600003, 721.5, 74, ''], [1167.9852429600003, 720.5, 1218.9852429600003, 741.5, 76, None], [1222.9852429600003, 720.5, 1273.9852429600003, 741.5, 76, None], [1302.9852429600003, 720.5, 1523.9852429600003, 741.5, 76, ''], [1167.9852429600003, 740.5, 1218.9852429600003, 761.5, 78, None], [1222.9852429600003, 740.5, 1273.9852429600003, 761.5, 78, None], [1302.9852429600003, 740.5, 1523.9852429600003, 761.5, 78, ''], [1167.9852429600003, 760.5, 1218.9852429600003, 781.5, 80, None], [1222.9852429600003, 760.5, 1273.9852429600003, 781.5, 80, None], [1302.9852429600003, 760.5, 1523.9852429600003, 781.5, 80, ''], [1167.9852429600003, 780.5, 1218.9852429600003, 801.5, 81, None], [1222.9852429600003, 780.5, 1273.9852429600003, 801.5, 81, None], [1302.9852429600003, 780.5, 1523.9852429600003, 801.5, 81, ''], [1167.9852429600003, 800.5, 1218.9852429600003, 821.5, 88, None], [1222.9852429600003, 800.5, 1273.9852429600003, 821.5, 88, None], [1302.9852429600003, 800.5, 1523.9852429600003, 821.5, 88, ''], [1167.9852429600003, 820.5, 1218.9852429600003, 841.5, 89, None], [1222.9852429600003, 820.5, 1273.9852429600003, 841.5, 89, None], [1302.9852429600003, 820.5, 1523.9852429600003, 841.5, 89, ''], [1167.9852429600003, 840.5, 1218.9852429600003, 861.5, 90, None], [1222.9852429600003, 840.5, 1273.9852429600003, 861.5, 90, None], [1302.9852429600003, 840.5, 1523.9852429600003, 861.5, 90, ''], [1167.9852429600003, 860.5, 1218.9852429600003, 881.5, 93, None], [1222.9852429600003, 860.5, 1273.9852429600003, 881.5, 93, None], [1302.9852429600003, 860.5, 1523.9852429600003, 881.5, 93, ''], [1167.9852429600003, 880.5, 1218.9852429600003, 901.5, 94, None], [1222.9852429600003, 880.5, 1273.9852429600003, 901.5, 94, None], [1302.9852429600003, 880.5, 1523.9852429600003, 901.5, 94, ''], [1167.9852429600003, 900.5, 1218.9852429600003, 921.5, 95, None], [1222.9852429600003, 900.5, 1273.9852429600003, 921.5, 95, None], [1302.9852429600003, 900.5, 1523.9852429600003, 921.5, 95, ''], [1167.9852429600003, 920.5, 1218.9852429600003, 941.5, 97, None], [1222.9852429600003, 920.5, 1273.9852429600003, 941.5, 97, None], [1302.9852429600003, 920.5, 1523.9852429600003, 941.5, 97, ''], [1167.9852429600003, 940.5, 1218.9852429600003, 961.5, 98, None], [1222.9852429600003, 940.5, 1273.9852429600003, 961.5, 98, None], [1302.9852429600003, 940.5, 1523.9852429600003, 961.5, 98, ''], [1167.9852429600003, 960.5, 1218.9852429600003, 981.5, 100, None], [1222.9852429600003, 960.5, 1273.9852429600003, 981.5, 100, None], [1302.9852429600003, 960.5, 1523.9852429600003, 981.5, 100, ''], [1167.9852429600003, 980.5, 1218.9852429600003, 1001.5, 103, None], [1222.9852429600003, 980.5, 1273.9852429600003, 1001.5, 103, None], [1302.9852429600003, 980.5, 1523.9852429600003, 1001.5, 103, ''], [1167.9852429600003, 1000.5, 1218.9852429600003, 1021.5, 104, None], [1222.9852429600003, 1000.5, 1273.9852429600003, 1021.5, 104, None], [1302.9852429600003, 1000.5, 1523.9852429600003, 1021.5, 104, ''], [1167.9852429600003, 1020.5, 1218.9852429600003, 1041.5, 106, None], [1222.9852429600003, 1020.5, 1273.9852429600003, 1041.5, 106, None], [1302.9852429600003, 1020.5, 1523.9852429600003, 1041.5, 106, ''], [1167.9852429600003, 1040.5, 1218.9852429600003, 1061.5, 108, None], [1222.9852429600003, 1040.5, 1273.9852429600003, 1061.5, 108, None], [1302.9852429600003, 1040.5, 1523.9852429600003, 1061.5, 108, ''], [1167.9852429600003, 1060.5, 1218.9852429600003, 1081.5, 109, None], [1222.9852429600003, 1060.5, 1273.9852429600003, 1081.5, 109, None], [1302.9852429600003, 1060.5, 1523.9852429600003, 1081.5, 109, ''], [1167.9852429600003, 1080.5, 1218.9852429600003, 1101.5, 111, None], [1222.9852429600003, 1080.5, 1273.9852429600003, 1101.5, 111, None], [1302.9852429600003, 1080.5, 1523.9852429600003, 1101.5, 111, ''], [1167.9852429600003, 1100.5, 1218.9852429600003, 1121.5, 114, None], [1222.9852429600003, 1100.5, 1273.9852429600003, 1121.5, 114, None], [1302.9852429600003, 1100.5, 1523.9852429600003, 1121.5, 114, ''], [1167.9852429600003, 1120.5, 1218.9852429600003, 1141.5, 116, None], [1222.9852429600003, 1120.5, 1273.9852429600003, 1141.5, 116, None], [1302.9852429600003, 1120.5, 1523.9852429600003, 1141.5, 116, ''], [1167.9852429600003, 1140.5, 1218.9852429600003, 1161.5, 117, None], [1222.9852429600003, 1140.5, 1273.9852429600003, 1161.5, 117, None], [1302.9852429600003, 1140.5, 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import pandas as pd
from cocoatree.io import load_MSA, load_tree_ete3
from cocoatree.visualization import update_tree_ete3_and_return_style


annot_file = 'data/random_seq_tree_annotations.csv'
df_annot = pd.read_csv(annot_file)

tree_file = 'data/random_seq_tree_kpicsg_ete3.treefile'
tree_ete3 = load_tree_ete3(tree_file)

sector_file = 'data/SCA_sector_1_core_tagged_seq.fasta'
data = load_MSA(sector_file, 'fasta')

sector_id = data["sequence_ids"]
sector_seq = data["alignment"]


colors = {
    "Bacteria": "black",
    "Eukaryota": "#cccccc",
    "FMO_Cyano": "#fff5f0",
    "UbiL": "#fdd4c2",
    "UbiI": "#fca082",
    "UbiH": "#fb694a",
    "UbiF": "#e32f27",
    "UbiN": "#b11218",
    "UbiFHILM_Cyano": "#67000d",
    }


tree_style, column_layout = update_tree_ete3_and_return_style(
    tree_ete3, df_annot, sector_id, sector_seq,
    meta_data=("superkingdom", "HMM_annotation"),
    fig_title='Visualization example',
    metadata_colors=colors,
    linewidth=3,
    show_leaf_name=False,
    t_sector_seq=True,
    t_sector_heatmap=False,
    colormap='inferno'
    )


tree_ete3.render("sector_phylogeny_colors.png", tree_style=tree_style)