UpPair

Easy to use python tool to visualize intersection between paired groups.

Setup and Installation

UpPair will be available on pypi soon to be installed via pip

pip install UpPair

Alternatively, if you prefer anaconda

conda install UpPair

Introduction

Where UpSet plots were created to solve the problem of the over complicated Venn Diagram with multiple sets overlapping, UpPair is designed to solve the issue of sequential paired Venn Diagrams.

On its own a Venn diagram is satisfactory in displaying data; however, if the diagrams are related to one another and one wanted to compare them as to visualize a comparison between the groupings, they are essentially unhelpful both for visualizing absolute numbers and relative overlap ratios. UpPair plots allow you maintain all the data demonstrated in a Venn, while allowing you to orient each pairing in a way that compairing between them is simple and intuitive. The best part is that with our tool, you can create these plots with only 1 line of code and with straightforward easy to use cusomtizations.

Examples:

• Examples could function as good strating points when created your own plot. Once your data is formatted properly, you can used the command used to create the figure that would best capture your data and adjust setting accordingly.
• All examples show figures frmatted with Biomedical data. UpPair certainly is not limited to these use cases.
• All data used for display was generated randomly and should not be used to infer any biological phenomena.

Example 1: Basic Plot

• Visualize the overlap of replicate samples from the same patient sequenced separaltey

Example 2:

• Comparing methodologies on same sample

Example 3: Two features stacked

Example 4: Grouping of 3 samples.

• Figure shows intersection of somatic mutation identified in various biopsies in the same individual. Includes sample IDs.

Example 5:

• Figure shows comparison of two methods (CTC and cfDNA) to detect somatic mutations compared with biopsy. Both methods are compared only with against biopsy (treated as gold-standard) and sensitivity and specifity is displayed. Results are compared across multiple cancer types to determine if a given method would perform better in a certain cancer type.

Example 6:

• Figure shows results from a single patient over the course of a few years. It displays the consistency between somatic mutations dected from cfDNA and CTC collections. It also shows their relationship with two biomarkers over the course of various treatments.

Documentation

For full documentation and instructions on customizations please see User Manual