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%run GLOBALS.py
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import matplotlib as mpl
mpl.use('TkAgg')
import matplotlib.pyplot as plt
%matplotlib inline
import pandas as pd
import seaborn as sns
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import abundance_plot_utils
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burkhold = {'Order':['Burkholderiales']}
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list(burkhold.keys())
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list(burkhold.values())[0]
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data_reduced = pd.read_csv(MAIN_DIR + "/results/reduced_data--all_taxonomy_remains.csv")
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data_reduced.columns
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tmp = ['Kingdom', 'Phylum', 'Class', 'Order', 'Family', 'Genus']
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abundance_plot_utils.taxonomy_levels_above(taxa_level='Order')
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abundance_plot_utils.taxonomy_levels_below(taxa_level='Order')
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abundance_plot_utils.label_from_taxa_colnames('Dog', 'Cat', 'Rat')
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abundance_plot_utils.taxa_dict_to_descriptive_string(burkhold)
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list(burkhold.values())[0][0]
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abundance_plot_utils.heatmap_all_below(dataframe = data_reduced,
taxa_dict = burkhold,
main_dir = MAIN_DIR,
plot_dir ='plots/drill_down',
)
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abundance_plot_utils.heatmap_all_below(dataframe = data_reduced,
taxa_dict = burkhold,
main_dir = MAIN_DIR,
plot_dir='plots/drill_down',
low_cutoff = 0.01)
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bacteroid = {'Phylum':['Bacteroidetes']}
abundance_plot_utils.heatmap_all_below(dataframe = data_reduced,
taxa_dict = bacteroid,
plot_dir='plots/drill_down')
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bacteroid = {'Phylum':['Bacteroidetes']}
abundance_plot_utils.heatmap_all_below(dataframe = data_reduced,
taxa_dict = bacteroid,
plot_dir='plots/drill_down',
low_cutoff = 0.005)
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import abundance_utils
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toy = data_reduced.head()
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toy
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abundance_plot_utils.heatmap_all_below(dataframe = data_reduced,
taxa_dict = {'Order':['Myxococcales']},
main_dir = MAIN_DIR,
plot_dir='plots/drill_down',
low_cutoff = 0)
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# Bdellovibrionales
abundance_plot_utils.heatmap_all_below(dataframe = data_reduced,
taxa_dict = {'Order':['Bdellovibrionales']},
main_dir = MAIN_DIR,
plot_dir='plots/drill_down',
low_cutoff = 0)
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