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PCA plot introduction ​

The PCA (Principal Component Analysis) plot in Omics Studio provides a powerful visual tool for exploring and understanding the variance within your dataset. By reducing the dimensionality of complex data, it enables the identification of patterns and clusters, facilitating deeper insights into the underlying biological processes. This plot is instrumental in revealing the relative relationships between samples, genes, or other entities, making it invaluable for transcriptomics and proteomics studies.

When to use the PCA plot ​

Usually, we use PCA plots to explore whether the main variance in the data behaves as expected, e.g., if replicates are located close to each other. Using PCA plots, it is also often investigated whether PC1, representing the most variation in the data, or PC2, representing the second most variation in the data, seems to be able to separate groups within the samples or consistent with batches and other experimental factors. In Omics Studio, you also have the opportunity to compare a PCA plot filtered according to chosen pathways in Pathway Graph or one of your lists from My Lists with the unfiltered PCA plot.

Get started ​

Select your data source: Initiate your analysis by determining the source of the data to be visualized in the PCA plot, unless you just want to expect the unfiltered PCA plot. There are two main filtration options available:

  1. Pathway graph: This option displays all nodes within the context of the selected pathways from the Pathway Graph.
  2. My lists: This alternative focuses on nodes specified by the My lists. If used, remember to select the desired custom list for visualization.

💡 If blank PCA plot

For the Pathway graph option; if the PCA plot appears blank (shows nothing), follow these steps:

  1. Navigate to the Pathway graph.
  2. Choose the relevant pathways.
  3. Return to the PCA plot, and the visualization should now be populated.

Tools in the PCA plot ​

The PCA plot in Omics Studio is equipped with a suite of interactive tools designed to enhance your data analysis experience. You can click on the different Group name (top right corner of the plot) to hide them. When clicked on, the Group name will turn transparent. You can reintroduce the group by clicking a second time.

If you hoover on the plot, additional interactive tools will appear:

  • 📸 Download: Capture and save the current view of the plot as a PNG file, allowing for easy sharing and documentation.
  • 🔍 Zoom: Focus on a specific area of the plot for a closer look.
  • 🍳 Pan: Navigate across the plot to explore different sections by clicking and dragging.
  • 🔲 Box Select: Use a rectangular selection box to highlight and examine specific nodes within the plot.
  • ➕ Zoom In
  • ➖ Zoom Out
  • 🤠 Lasso Select: With the lasso tool, draw freeform shapes to select nodes, offering precision in isolating areas of interest.
  • 💠 Autoscale: Automatically adjust the plot view to ensure all nodes are visible, optimizing your analysis.
  • 🏠 Reset Axes: Revert any zoom and pan adjustments to their original state, providing a fresh perspective.