我一直在研究ete3
的包装器,我可以自定义叶标签(即哪些叶子显示标签)和节点存在(即显示哪些叶节点)。我遇到问题的一个部分是定义标签大小。
当我尝试更改fsize
中的TextFace
时,没有真正发生的事情:(我遇到了一个奇怪的怪癖,我的实际数据中标签很大,树很小。
我无法获得实际树形图的比例和标签一起工作以形成一个有凝聚力的数字。
以下是无法更改iris
数据集上的标签大小的示例
下面附有3种不同的标签尺寸:1, 1e2, and 1e4
import pandas as pd
from sklearn.datasets import load_iris
import ete3
# Get data
X = pd.DataFrame(load_iris().data, columns=[load_iris().feature_names], index=["iris_%d"%_ for _ in range(150)])
DF_dism = 1 - X.T.corr()
# outside program to create newick tree
tree_str = '(((((((((((iris_105:0.015466,iris_104:0.015466):0.002489,iris_128:0.017954):0.051900,iris_134:0.069854):0.014699,iris_106:0.084554):0.029907,((((iris_113:0.008951,iris_108:0.008951):0.007140,iris_114:0.016091):0.020324,iris_132:0.036415):0.015510,iris_122:0.051925):0.062536):0.154083,iris_100:0.268544):0.059595,((((iris_143:0.029031,iris_130:0.029031):0.035661,iris_121:0.064692):0.035647,((((iris_142:0.000000,iris_101:0.000000):0.010308,iris_107:0.010308):0.023017,iris_119:0.033325):0.027399,iris_103:0.060724):0.039616):0.060280,(((((iris_111:0.010695,iris_102:0.010695):0.004910,iris_140:0.015606):0.019544,iris_144:0.035150):0.021438,(iris_146:0.026679,iris_135:0.026679):0.029909):0.013635,iris_136:0.070223):0.090396):0.167519):0.152880,((((((iris_137:0.036573,iris_117:0.036573):0.005650,(iris_116:0.021554,iris_109:0.021554):0.020669):0.014556,((iris_125:0.016457,iris_124:0.016457):0.013361,(iris_149:0.013347,iris_148:0.013347):0.016472):0.026961):0.015363,(iris_120:0.052702,iris_112:0.052702):0.019440):0.019892,iris_83:0.092034):0.090205,(((((iris_147:0.019669,iris_123:0.019669):0.025376,iris_139:0.045045):0.004471,iris_133:0.049517):0.038807,(iris_145:0.046706,iris_68:0.046706):0.041617):0.003435,((iris_129:0.034158,iris_72:0.034158):0.018834,iris_115:0.052993):0.038766):0.090480):0.298780):0.446896,iris_118:0.927915):0.171235,(((((((((iris_89:0.019602,iris_78:0.019602):0.012196,iris_94:0.031798):0.021078,(iris_62:0.024576,iris_54:0.024576):0.028300):0.019265,(iris_76:0.021066,iris_60:0.021066):0.051074):0.033419,(iris_91:0.061458,iris_52:0.061458):0.044101):0.073034,((((((iris_73:0.015746,iris_55:0.015746):0.007907,iris_70:0.023653):0.017085,iris_63:0.040738):0.033484,(iris_77:0.026480,iris_53:0.026480):0.047742):0.021259,iris_84:0.095481):0.008300,iris_66:0.103781):0.074812):0.095629,((((iris_131:0.025100,iris_127:0.025100):0.033935,iris_126:0.059035):0.040224,((iris_138:0.040319,iris_110:0.040319):0.005869,iris_90:0.046188):0.053071):0.017816,(iris_141:0.074887,iris_87:0.074887):0.042187):0.157148):0.215498,(((((iris_93:0.013769,iris_71:0.013769):0.008009,iris_65:0.021777):0.053482,iris_57:0.075259):0.036176,(((iris_88:0.024950,iris_85:0.024950):0.038041,iris_95:0.062991):0.011447,((((iris_75:0.013694,iris_50:0.013694):0.013866,iris_51:0.027560):0.005357,iris_82:0.032917):0.006739,(iris_74:0.022758,iris_61:0.022758):0.016898):0.034782):0.036997):0.085015,((((iris_99:0.015603,iris_67:0.015603):0.011335,(iris_96:0.010209,iris_56:0.010209):0.016730):0.031396,(iris_97:0.016052,iris_81:0.016052):0.042283):0.030065,(((iris_80:0.014517,iris_58:0.014517):0.019641,iris_59:0.034158):0.018663,((iris_92:0.016236,iris_86:0.016236):0.008542,iris_69:0.024778):0.028044):0.035579):0.108050):0.293270):0.285865,((iris_79:0.123616,iris_64:0.123616):0.124095,iris_98:0.247711):0.527874):0.323564):2.691791,((((iris_41:0.252019,iris_25:0.252019):0.163686,(((((iris_29:0.022655,iris_8:0.022655):0.021997,iris_3:0.044652):0.003728,iris_45:0.048380):0.042574,((iris_12:0.021454,iris_1:0.021454):0.024231,iris_23:0.045685):0.045269):0.048283,(((iris_30:0.015235,iris_20:0.015235):0.026412,((iris_34:0.000000,iris_9:0.000000):0.000000,iris_37:0.000000):0.041647):0.030817,iris_24:0.072463):0.066774):0.276467):0.140239,((((((((iris_39:0.009341,iris_18:0.009341):0.008969,iris_26:0.018311):0.020329,iris_11:0.038639):0.016404,((iris_28:0.016981,iris_27:0.016981):0.013305,(iris_49:0.016905,iris_7:0.016905):0.013381):0.024757):0.022419,iris_31:0.077462):0.013526,((iris_47:0.027609,iris_38:0.027609):0.019907,iris_44:0.047516):0.043472):0.107130,(((iris_17:0.027138,iris_5:0.027138):0.025207,((iris_48:0.018085,iris_0:0.018085):0.007010,iris_43:0.025096):0.027249):0.032517,((iris_36:0.008628,iris_35:0.008628):0.032997,(iris_10:0.006140,iris_2:0.006140):0.035485):0.043237):0.113256):0.120936,((((iris_40:0.016634,iris_21:0.016634):0.014411,iris_6:0.031045):0.046044,iris_19:0.077089):0.029864,(((iris_42:0.018855,iris_13:0.018855):0.014108,iris_46:0.032962):0.011022,iris_4:0.043984):0.062968):0.212102):0.236889):0.303087,(((((iris_33:0.060688,iris_16:0.060688):0.035284,iris_32:0.095972):0.034956,iris_14:0.130928):0.063009,iris_15:0.193936):0.224991,iris_22:0.418928):0.440103):2.931910);'
# ete3 tree
tree = ete3.Tree(tree_str)
# Annotate tree
node_size = 10
label_size = 10000
for node in tree.traverse():
if node.is_leaf():
node.img_style["size"] = node_size
# Show leaf labels
name_face = ete3.TextFace(node.name, fgcolor="black", fsize=label_size)
node.add_face(name_face, column=0, position='branch-right')
# Circular Style
ts = ete3.TreeStyle()
ts.show_branch_length = True # show branch length
ts.show_scale = True
ts.mode = "c" # "c" is circular mode
ts.show_leaf_name = False
ts.show_scale = False
tree.render("%%inline", dpi=300, tree_style=ts, w=500)