Note
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Simple tree visualization with metadata¶
This example details how to plot a simple tree visualization with cocoatree.
from cocoatree.io import load_tree_ete3
from cocoatree.datasets import load_S1A_serine_proteases
from cocoatree.visualization import update_tree_ete3_and_return_style
Load metadata¶
We use the S1A serine protease dataset that is included in cocoatree but you can use your own metadata by importing a csv file as a pandas dataframe.
For more details on the S1A serine proteases dataset, go to S1A serine proteases.
serine_dataset = load_S1A_serine_proteases('halabi')
df_annot = serine_dataset["metadata"]
print(df_annot)
Seq_ID ... Family
0 4139558 ... Muridae
1 7546312 ... Suidae
2 230004 ... Hominidae
3 4139720 ... Hominidae
4 10835843 ... Muridae
... ... ... ...
1465 54641874 ... Drosophilidae
1466 55236641 ... Culicidae
1467 55238595 ... Culicidae
1468 66772117 ... Drosophilidae
1469 24660124 ... Drosophilidae
[1470 rows x 14 columns]
Note
The dataframe must have a Seq_ID column with identifiers that are
identical to the ones in the MSA (although no MSA is needed in the
present example), and in the newick tree.:
Load tree file¶
Use cocoatree.io.load_tree_ete3() dedicated function
tree_file = 'data/halabi_82_seqs.txt'
tree_ete3 = load_tree_ete3(tree_file)
print(tree_ete3)
/-2462649
/-|
| \-10089
|
/-| /-432990
| | |
| | | /-2353161
| \-| |
| | | /-62082405
| | | /-|
| \-| | | /-87248295
| | | \-|
| | | \-95102864
| | |
| \-| /-8037814
| | /-|
| | | | /-2463064
| | | \-|
| | | \-7248890
| \-|
| | /-62082401
| | /-|
/-| | | \-62082397
| | | |
| | \-| /-29501764
| | | /-|
| | | | \-8037817
| | \-|
| | | /-609526
| | \-|
| | | /-8037819
| | \-|
| | | /-2463076
| | \-|
/-| | | /-8037826
| | | \-|
| | | | /-2463092
| | | \-|
| | | \-8037824
| | |
| | | /-47078376
| | \-|
| | | /-62546195
/-| | \-|
| | | \-4210802
| | |
| | | /-91088279
| | \-|
| | | /-4530062
| | \-|
| | \-51557679
| |
| | /-91088171
| \-|
| \-1160388
|
| /-1326386
| |
| | /-2642189
| | |
| | | /-50753637
--| | | /-|
| | | | | /-16758930
| | | | \-|
| | | | | /-73957472
| | | /-| \-|
| | | | | \-62897905
| | | | |
| | /-| | | /-68381018
| | | | | \-|
| | | | | | /-5441859
| | | | | \-|
| | | | | \-48526114
| | | | |
| | | | | /-1706190
| | | | | /-|
| | | | | | | /-47086795
| | | | | | \-|
| | | \-| | | /-468751
\-| | | | \-|
| | | | | /-48526112
| | | /-| \-|
| | | | | \-5441861
| | | | |
| | | | | /-62738027
| | | | | /-|
| | | | | | \-117615
| | | | \-|
| | | | | /-73957004
| | | | | |
| | | | \-| /-75991694
| | \-| | /-|
| | | | | \-117616
| | | \-|
| | | | /-73957010
| | | \-|
| | | | /-73957387
| | | \-|
| | | \-76639924
| | |
| | | /-56971185
| | \-|
| | \-57870463
\-|
| /-89266985
| /-|
| | \-56693556
| |
| /-| /-33187750
| | | |
| | | | /-1942486
| | | | /-|
| | \-| | \-61845170
| | | /-|
| | | | | /-76443665
| | | | \-|
| | \-| \-2196868
| /-| |
| | | | /-73950880
| | | \-|
| | | \-73950882
| | |
| | | /-22532097
| | | |
| | | | /-73959449
| | | | /-|
| | \-| | | /-73978296
| | | | \-|
| | | | | /-62655772
| | | | \-|
| | \-| \-19353198
| | |
| | | /-6103633
| | | /-|
| | | | | /-6755819
| | | | \-|
| | \-| \-27763826
| | |
| | | /-47523252
\-| | |
| \-| /-4753835
| | |
| | | /-27806375
| \-| /-|
| | | | /-1588661
| | | \-|
| \-| \-1332447
| |
| | /-31711394
| | |
| \-| /-47523468
| | /-|
| | | \-136434
| \-|
| | /-1717790
| \-|
| | /-88192901
| \-|
| \-50960668
|
| /-82407844
\-|
\-68372817
See also
Check sphx_glr_auto_examples_a_quick_start_plot_load_tree.py for details on the Newick format that is accepted.
Plot figure¶
Create the tree style that will be applied to your tree with
cocoatree.visualization.update_tree_ete3_and_return_style()
tree_style, column_layout = update_tree_ete3_and_return_style(
tree_ete3, df_annot,
meta_data=('Protein_type', 'Subphylum', 'Class'),
fig_title='A tree visualization with metadata',
)
Save the figure:
tree_ete3.render("simple_tree.png", tree_style=tree_style)
{'nodes': [[243.61484, 15.5, 254.61484, 26.5, 5, None], [241.01792, 108.91796875, 252.01792, 119.91796875, 10, None], [353.63012, 115.5, 364.63012, 126.5, 15, None], [363.97738, 160.5, 374.97738, 171.5, 19, None], [400.66537999999997, 175.5, 411.66537999999997, 186.5, 21, None], [325.32417999999996, 247.84375, 336.32417999999996, 258.84375, 24, None], [458.9671799999999, 215.5, 469.9671799999999, 226.5, 25, None], [352.35115999999994, 280.1875, 363.35115999999994, 291.1875, 28, None], [379.65863999999993, 255.5, 390.65863999999993, 266.5, 29, None], [384.9161199999999, 324.25, 395.9161199999999, 335.25, 34, None], [405.58595999999994, 343.0, 416.58595999999994, 354.0, 36, None], [422.0677999999999, 360.5, 433.0677999999999, 371.5, 38, None], [438.1107399999999, 375.5, 449.1107399999999, 386.5, 40, None], [142.369, 420.5, 153.369, 431.5, 43, None], [168.90834, 435.5, 179.90834, 446.5, 45, None], [203.19488, 661.75, 214.19488, 672.75, 62, None], [238.41168000000002, 623.0, 249.41168000000002, 634.0, 63, None], [303.25728000000004, 640.5, 314.25728000000004, 651.5, 65, None], [322.92968, 655.5, 333.92968, 666.5, 67, None], [236.56988, 700.5, 247.56988, 711.5, 70, None], [270.31988, 715.5, 281.31988, 726.5, 72, None], [220.56552, 764.25, 231.56552, 775.25, 77, None], [245.7475, 783.0, 256.7475, 794.0, 79, None], [271.36056, 800.5, 282.36056, 811.5, 81, None], [290.81426, 815.5, 301.81426, 826.5, 83, None], [234.90251999999998, 883.625, 245.90251999999998, 894.625, 86, None], [274.37352, 855.5, 285.37352, 866.5, 87, None], [263.4264, 911.75, 274.4264, 922.75, 90, None], [284.62942, 938.0, 295.62942, 949.0, 92, None], [306.37406, 915.5, 317.37406, 926.5, 93, None], [303.73758, 960.5, 314.73758, 971.5, 96, None], [360.04857999999996, 975.5, 371.04857999999996, 986.5, 98, None], [212.99276, 1015.5, 223.99276, 1026.5, 101, None], [341.89189999999996, 1165.5, 352.89189999999996, 1176.5, 112, None], [394.43229999999994, 1115.5, 405.43229999999994, 1126.5, 114, None], [364.93095999999997, 1195.5, 375.93095999999997, 1206.5, 120, None], [140.03877999999997, 1319.9140625, 151.03877999999997, 1330.9140625, 125, None], [169.55305999999996, 1263.0, 180.55305999999996, 1274.0, 126, None], [243.96925999999996, 1280.5, 254.96925999999996, 1291.5, 128, None], [322.54465999999996, 1295.5, 333.54465999999996, 1306.5, 130, None], [190.49478, 1376.828125, 201.49478, 1387.828125, 133, None], [310.42157999999995, 1340.5, 321.42157999999995, 1351.5, 134, None], [361.30598, 1355.5, 372.30598, 1366.5, 136, None], [257.12138, 1413.15625, 268.12138, 1424.15625, 139, None], [358.04798, 1440.8125, 369.04798, 1451.8125, 141, None], [389.61132000000003, 1440.5, 400.61132000000003, 1451.5, 144, None], [406.39598, 1455.5, 417.39598, 1466.5, 146, None], [415.55986000000007, 1560.5, 426.55986000000007, 1571.5, 155, None], [456.80426000000006, 1575.5, 467.80426000000006, 1586.5, 157, None]], 'faces': [[284.62724, 3.0, 339.62724, 19.0, 6, '2462649'], [607.51932, 0.5, 658.51932, 21.5, 6, None], [662.51932, 0.5, 713.51932, 21.5, 6, None], [717.51932, 0.5, 768.51932, 21.5, 6, None], [275.59984, 23.0, 314.59984, 39.0, 7, '10089'], [607.51932, 20.5, 658.51932, 41.5, 7, None], [662.51932, 20.5, 713.51932, 41.5, 7, None], [717.51932, 20.5, 768.51932, 41.5, 7, None], [308.72052, 43.0, 355.72052, 59.0, 9, '432990'], [607.51932, 40.5, 658.51932, 61.5, 9, None], [662.51932, 40.5, 713.51932, 61.5, 9, None], [717.51932, 40.5, 768.51932, 61.5, 9, None], [391.57292, 63.0, 446.57292, 79.0, 11, '2353161'], [607.51932, 60.5, 658.51932, 81.5, 11, None], [662.51932, 60.5, 713.51932, 81.5, 11, None], [717.51932, 60.5, 768.51932, 81.5, 11, None], [450.19291999999996, 83.0, 513.19292, 99.0, 14, '62082405'], [607.51932, 80.5, 658.51932, 101.5, 14, None], [662.51932, 80.5, 713.51932, 101.5, 14, None], [717.51932, 80.5, 768.51932, 101.5, 14, None], [540.01932, 103.0, 603.01932, 119.0, 16, '87248295'], [607.51932, 100.5, 658.51932, 121.5, 16, None], [662.51932, 100.5, 713.51932, 121.5, 16, None], [717.51932, 100.5, 768.51932, 121.5, 16, None], [431.00651999999997, 123.0, 494.00651999999997, 139.0, 17, '95102864'], [607.51932, 120.5, 658.51932, 141.5, 17, None], [662.51932, 120.5, 713.51932, 141.5, 17, None], [717.51932, 120.5, 768.51932, 141.5, 17, None], [402.21238, 143.0, 457.21238, 159.0, 20, '8037814'], [607.51932, 140.5, 658.51932, 161.5, 20, None], [662.51932, 140.5, 713.51932, 161.5, 20, None], [717.51932, 140.5, 768.51932, 161.5, 20, None], [431.24465999999995, 163.0, 486.24465999999995, 179.0, 22, '2463064'], [607.51932, 160.5, 658.51932, 181.5, 22, None], [662.51932, 160.5, 713.51932, 181.5, 22, None], [717.51932, 160.5, 768.51932, 181.5, 22, None], [422.52691999999996, 183.0, 477.52691999999996, 199.0, 23, '7248890'], [607.51932, 180.5, 658.51932, 201.5, 23, None], [662.51932, 180.5, 713.51932, 201.5, 23, None], [717.51932, 180.5, 768.51932, 201.5, 23, None], [481.19197999999994, 203.0, 544.19198, 219.0, 26, '62082401'], [607.51932, 200.5, 658.51932, 221.5, 26, None], [662.51932, 200.5, 713.51932, 221.5, 26, None], [717.51932, 200.5, 768.51932, 221.5, 26, None], [481.93351999999993, 223.0, 544.9335199999999, 239.0, 27, '62082397'], [607.51932, 220.5, 658.51932, 241.5, 27, None], [662.51932, 220.5, 713.51932, 241.5, 27, None], [717.51932, 220.5, 768.51932, 241.5, 27, None], [422.5176399999999, 243.0, 485.5176399999999, 259.0, 30, '29501764'], [607.51932, 240.5, 658.51932, 261.5, 30, None], [662.51932, 240.5, 713.51932, 261.5, 30, None], [717.51932, 240.5, 768.51932, 261.5, 30, None], [444.53083999999996, 263.0, 499.53083999999996, 279.0, 31, '8037817'], [607.51932, 260.5, 658.51932, 281.5, 31, None], [662.51932, 260.5, 713.51932, 281.5, 31, None], [717.51932, 260.5, 768.51932, 281.5, 31, None], [455.0013399999999, 283.0, 502.0013399999999, 299.0, 33, '609526'], [607.51932, 280.5, 658.51932, 301.5, 33, None], [662.51932, 280.5, 713.51932, 301.5, 33, None], [717.51932, 280.5, 768.51932, 301.5, 33, None], 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583.0, 554.2142799999999, 599.0, 60, '2642189'], [607.51932, 580.5, 658.51932, 601.5, 60, None], [662.51932, 580.5, 713.51932, 601.5, 60, None], [717.51932, 580.5, 768.51932, 601.5, 60, None], [325.74448000000007, 603.0, 388.74448000000007, 619.0, 64, '50753637'], [607.51932, 600.5, 658.51932, 621.5, 64, None], [662.51932, 600.5, 713.51932, 621.5, 64, None], [717.51932, 600.5, 768.51932, 621.5, 64, None], [329.20794, 623.0, 392.20794, 639.0, 66, '16758930'], [607.51932, 620.5, 658.51932, 641.5, 66, None], [662.51932, 620.5, 713.51932, 641.5, 66, None], [717.51932, 620.5, 768.51932, 641.5, 66, None], [354.17304, 643.0, 417.17304, 659.0, 68, '73957472'], [607.51932, 640.5, 658.51932, 661.5, 68, None], [662.51932, 640.5, 713.51932, 661.5, 68, None], [717.51932, 640.5, 768.51932, 661.5, 68, None], [347.21558000000005, 663.0, 410.21558000000005, 679.0, 69, '62897905'], [607.51932, 660.5, 658.51932, 681.5, 69, None], [662.51932, 660.5, 713.51932, 681.5, 69, None], [717.51932, 660.5, 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1141.0], 117: [370.59669999999994, 1141.0, 497.0242599999999, 1181.0], 118: [386.80845999999997, 1141.0, 497.02425999999997, 1161.0], 119: [386.80845999999997, 1161.0, 466.50005999999996, 1181.0], 120: [353.39189999999996, 1181.0, 448.53548, 1221.0], 121: [376.43095999999997, 1181.0, 448.53548, 1201.0], 122: [376.43095999999997, 1201.0, 439.43141097999995, 1221.0], 123: [68.78338, 1221.0, 569.90926, 1601.0], 124: [113.42177999999998, 1221.0, 432.57777999999996, 1241.0], 125: [113.42177999999998, 1241.0, 569.90926, 1601.0], 126: [151.53877999999997, 1241.0, 569.90926, 1321.0], 127: [181.05305999999996, 1241.0, 434.45705999999996, 1261.0], 128: [181.05305999999996, 1261.0, 569.90926, 1321.0], 129: [255.46925999999996, 1261.0, 569.90926, 1281.0], 130: [255.46925999999996, 1281.0, 416.29411999999996, 1321.0], 131: [334.04465999999996, 1281.0, 411.02817999999996, 1301.0], 132: [334.04465999999996, 1301.0, 416.29411999999996, 1321.0], 133: [151.53877999999997, 1321.0, 541.38306, 1601.0], 134: [201.99478, 1321.0, 449.54474, 1381.0], 135: [321.92157999999995, 1321.0, 406.29238, 1341.0], 136: [321.92157999999995, 1341.0, 449.54473999999993, 1381.0], 137: [372.80598, 1341.0, 446.23848, 1361.0], 138: [372.80598, 1361.0, 449.54474, 1381.0], 139: [201.99478, 1381.0, 541.38306, 1601.0], 140: [268.62138, 1381.0, 470.38018, 1401.0], 141: [268.62138, 1401.0, 541.38306, 1601.0], 142: [369.54798, 1401.0, 451.55938000000003, 1421.0], 143: [369.54798, 1421.0, 541.38306, 1601.0], 144: [373.81454, 1421.0, 472.8961895, 1481.0], 145: [401.11132000000003, 1421.0, 467.08878000000004, 1441.0], 146: [401.11132000000003, 1441.0, 472.89618950000005, 1481.0], 147: [417.89598, 1441.0, 472.8961895, 1461.0], 148: [417.89598, 1461.0, 472.8961895, 1481.0], 149: [373.81454, 1481.0, 541.38306, 1601.0], 150: [398.77714000000003, 1481.0, 496.95894000000004, 1501.0], 151: [398.77714000000003, 1501.0, 541.38306, 1601.0], 152: [405.73818000000006, 1501.0, 516.6810600000001, 1541.0], 153: [412.87366000000003, 1501.0, 516.68106, 1521.0], 154: [412.87366000000003, 1521.0, 501.02186000000006, 1541.0], 155: [405.73818000000006, 1541.0, 541.3830600000001, 1601.0], 156: [427.05986000000007, 1541.0, 541.3830600000001, 1561.0], 157: [427.05986000000007, 1561.0, 540.4891200000001, 1601.0], 158: [468.30426000000006, 1561.0, 539.8667800000001, 1581.0], 159: [468.30426000000006, 1581.0, 540.4891200000001, 1601.0], 160: [54.90806, 1601.0, 356.38026, 1641.0], 161: [92.82826, 1601.0, 347.16206, 1621.0], 162: [92.82826, 1621.0, 356.38026, 1641.0]}}
You can also use ete3’s tree.show() method for displaying the figure
in ete3’s interactive GUI.
Warning
If you wish to modify the style that has been applied to the
tree_ete3 object, you need to reload the tree in order to clear
out the previous tree style. Otherwise, there will be a
superimposition of tree styles.
Total running time of the script: (0 minutes 1.705 seconds)
