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Data Tables & Customization

Working with Data Tables

Throughout the platform, data tables are provided as expandable sections below visualizations. They are indicated by a header with a collapse/expand chevron (arrow) on the right side.

Expanding a table

Click anywhere on the table header row (e.g., "GO Enrichment Table", "Z-score Table", "PC Scores", "Genes — All", "KEGG Enrichment Table") to toggle it open or closed.

Table features

  • Tables display rows and columns of data corresponding to the plot above.
  • You can scroll horizontally within wide tables to see all columns.
  • You can scroll vertically to see all rows.
  • Column headers describe the data in each column (e.g., gene_id, sample names, PC scores, correlation values).

Tip

Data tables are a great way to verify specific values that you see in the plots, or to identify individual genes or samples of interest.

Customizing Plots

Liragen Insights gives you full control over plot appearance through the sidebar. Here is a typical customization workflow:

Adjusting Significance Thresholds

  1. In the sidebar Filters section, drag the Adjusted p-value threshold slider to set your desired significance cutoff (e.g., 0.05 for a standard cutoff, or 0.01 for a more stringent one).
  2. Drag the log2 Fold Change threshold slider to set the minimum fold change you consider biologically meaningful.
  3. Use the Top N slider to control how many top items appear in enrichment charts.
  4. All plots will update automatically to reflect the new thresholds.

Focusing on Specific Genes

  1. Use Filter by gene ID to narrow all visualizations to a specific set of genes.
  2. Alternatively, use Filter by gene desc to filter by functional description keywords.
  3. To highlight specific genes without removing others, use Highlight gene ID or Highlight genes desc.

Changing Plot Appearance

  1. Expand the Appearance section in the sidebar (click the header to toggle).
  2. Adjust Dot Size for scatter plot data points.
  3. Adjust Plot Height and Plot Width for chart dimensions.
  4. Click any Colors swatch to customize Up, Down, Select, Others, Title, BG, or Axis colors.
  5. Adjust Font size and Font color for text styling.
  6. Change Threshold Lines type and color for reference lines on the Volcano plot.

Resetting All Customizations

Click the "Reset to defaults" button at the bottom of the Appearance section to restore all settings to their original values.