A simple Python library for calculating Dissimilarity Overlap Curve and alpha/beta diversity
Project description
DOC analysis
A Python library for calculating Dissimilarity Overlap Curve and alpha/beta diversity for microbiome samples
Installation
pip install DO_analysis
Get started
How to plot DOC curve with this lib:
from DOC_analysis.DOC import DOC_with_plots
#upload ASV or abundance table as data, with columns as samples and rows as taxa
#upload metadata table with information about samples
#let metadata table have column of interest 'Group'
#Then simply run:
DOC_with_plots(data, metadata, 'Group')
Available functions
DOC.DOC_with_plots(data, metadata, feature, num_bins=50, sample_col='Sample') - plots DOC curve for each group and all groups combined
DOC.run_DOC_time(data, metadata, times, feature, time_col='Time', sample_col='Sample') - if you have longitudinal data, it will generate DOC plots across all time points and for each group
diversity.plot_diversity(data, metadata, feature, pairs=None, id_column='Sample', beta_metric="braycurtis", alfa_metric='shannon', plot_alpha=True, plot_beta=True) - to compute and plot alpha and beta diversity metrics
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