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October 4, 2019 12:46
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Generate iTOL "simple bar" annotation file from pandas dataframe
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import numpy as np | |
import pandas as pd | |
from ete3 import PhyloTree | |
def generate_simplebar(df: pd.DataFrame, save_file: str) -> None: | |
# df columns must be labels and values. | |
output = """DATASET_SIMPLEBAR\n | |
SEPARATOR COMMA\n | |
DATASET_LABEL,label_simplebar\n | |
COLOR,#ff0000\n | |
DATA\n"""+df.to_csv(header=False, index=False) | |
with open(save_file, "w") as f: | |
f.write(output) | |
tree = PhyloTree("tree.nwk") | |
leaf_labels = [leaf.name for leaf in tree.get_leaves()] | |
values = np.random.randint(0, 100, len(leaf_labels)).tolist() | |
generate_simplebar(pd.DataFrame([leaf_labels, values]).T, "bar.txt") |
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