Embedded Files
Our project goal was to implement a web-based pipeline for an already existing tool called Amplicon Architect, which is used to visualize focally amplified regions. Due to the specificity of this tool being specially designed for focal amplification oncogenic regions to elucidate the mechanisms of cancer biology, there exists only a couple other existing tools that characterize ecDNA from DAPI-stained images, such as ecDetect. Thus, our project involved a fundamental understanding of cancer biological pathways coupled with coding skills in web development (CSS) and data visualization (Python). With the utilization of such languages, the specific features and descriptive elements corresponding to each cancer sample inputted into the pipeline, along with the large amounts of output elicited by Amplicon Architect, can be better understood by users.
The overall design involved the implementation of various visualizations to provide specific statistics of the user’s corresponding cancer samples. Plotly is a Python library that enables the utilization of interactive and high-quality graphs that can be designed with an entire variety of colors. Specifically, the express module of Plotly enabled us to design these charts in an efficient and effective manner. These visualizations were included on the project view page of the tool to elicit insight into the distribution of the focal amplifications corresponding to each cancer cell line inputted by the user. Below are some of the visualizations we implemented for the page.
Pie chart displaying the percentage of cancer cell line samples having a specific focal amplification classification (ecDNA-red, breakage fusion-bridge (BFB)-green, complex non-cyclic-yellow, and linear-blue)
Hover feature that displays relevant information about a specific amplicon for the user, when hovered over such as oncogenes expressed over the specific amplicon or the maximum copy number.
Stacked bar chart displaying the number of focal amplifications each cancer cell line sample has, sorted by total number of ecDNA, then total number of BFB, total number of complex non-cyclic, and finally total number of linear (ecDNA-red, breakage fusion-bridge (BFB)-green, complex non-cyclic-yellow, and linear-blue)
Whole copy number plot demonstrating locations of amplicons across the ESO51 cell line from CCLE
The landing page for the website. This landing page features a description of AmpliconArchitect, some helpful information regarding AmpliconArchitect. It also features the Search bar, and underneath (not pictured) the projects that are loaded in.
Project Page overview. This table contains a button that can download the project data, as well as a list of all the samples within the project. This also contains a search bar for the samples table. In the future, this page will have project overview visualizations.
Sample View. This contains a button to download all the sample data. This view also contains the sample copy number plot filtered to contain only chromosomes with amplicons. Under the graph is a table that summarizes the features within that sample.
Leader: Devika
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