> For the complete documentation index, see [llms.txt](https://tbj128.gitbook.io/mian/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://tbj128.gitbook.io/mian/pcoa.md). # PCoA Creates a principal coordinate analysis (PCoA) graph at the selected taxonomic level based on the distance matrix generated by the selected metric ![](/files/-M3A394qBPCYwCtTUZnf) ### Used For * Visualizing the similarity between different samples ### Visualization Parameters #### Taxonomic Level The taxonomic level to aggregate the OTUs at. The OTUs will be grouped together (by summing the OTU values) at the selected taxonomic level before the analysis is applied. #### Categorical Variable Create comparative sample groups based on categorical variables uploaded in the metadata file. Optionally create a categorical variable from a quantitative variable by using the Quantile Range feature on the Projects home page. #### PCoA Type Choose from one or multiple distance measures #### Axis Range Define the range of the 3D PCA plot. Points falling outside of this range will be removed from the graph. ### Interactive Elements * Hover over each point to determine its sample ID and its principal component values * Rotate, zoom, and pan ### Additional Features * **Save Snapshot**: Save the visualization to the experiment notebook * **Download**: Downloads the visualization as a PNG file * **Share**: Creates a shareable link that allows you to share the visualization with others --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://tbj128.gitbook.io/mian/pcoa.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.