Summary

The pyphetools library provides code to create a summary of all of the phenopackets of a cohort. This can be useful to review work or understand the distribution of data. This page explains how to set up the notebook.

Imports

We first import several classes to visualize the data.

import pandas as pd
pd.set_option('display.max_colwidth', None) # show entire column contents, important!
from IPython.display import HTML, display
from pyphetools.visualization import *
import pyphetools
print(f"Using pyphetools version {pyphetools.__version__}")

Extract phenopackets

We then extract a list of phenopackets from the target directory.

ingestor = PhenopacketIngestor(indir="phenopackets")
ppkt_list = ingestor.get_phenopacket_list()

By default, pyphetools will create a new directory called phenopackets into which it will write the new phenopackets. Therefore, the PhenopacketIngestor will use phenopackets as a default if we do not specify the "indir" argument.

ingestor = PhenopacketIngestor()
ppkt_list = ingestor.get_phenopacket_list()

If the input directory contains phenopackets for more than one disease, an error message will appear. In this case, use the disease_id argument to specific the disease identifier.

Detailed table

The following command will display a table with the counts of annotated HPO terms for each PubMed identifier (publication) used in the cohort.

detailed_table = DetailedSupplTable(patient_list=ppkt_list)
display(HTML(detailed_table.get_html_table_by_pmid(min_count=1)))

pcharts

The PhenopacketCharts class uses matplotlib to display barcharts to show salient aspects of the data

This will display a chart with the counts of each disease in the cohort.

pcharts = PhenopacketCharts(indir="phenopackets")
pcharts.disease_barchart();

This will display a chart with the counts of individuals per publication (PMID) in the cohort.

pcharts.pmid_barchart();

And finally, this will display a chart with the most commonly annotated HPO terms in the cohort.

pcharts.most_common_hpo_terms(max_terms_to_show=10);