Plot Navigation panel

Plot Navigation panel

This panel provides users with options to navigate through the plots in the apps.

  1. Plot Type lets you select plot types to visualize your data:

    • Boxplot – Summarizes the distribution of data with median, quartiles, and whiskers.
    • Jitter Plot – Displays individual data points for better visibility of variation.
    • Violin Plot – Combines boxplot with kernel density to show data distribution.

  2. Plot Options: Users can choose from multiple plot types from the Plot type option for visualizing sequencing quality metrics such as Boxplot, Jitter Plot and Violin Plot With the help of Group By or Sort by option, users can group their visualization according to the various metadata variables such as “Plate, Tissue, Timepoint,etc”

  3. Quality Indicators lets you choose which alignment parameters to display in the plots (e.g., Number of input reads, Uniquely mapped reads, Average mapped length)

  4. Plot Design and Features:

    • Each QC parameter is displayed in a separate plot to ensure proper visualization of thresholds.
    • Y-axis: Represents the parameter values (e.g., Q30).
      • Scales are parameter-specific and automatically adjusted based on thresholds, with extra spacing for clarity.
    • X-axis: Displays sample groups based on metadata categories (e.g., Tissue, Timepoint, Concentration).
    • All samples can be displayed simultaneously by clicking and dragging over it to zoom in, ensuring a detailed overview.
    • Users can reset the axes using the small “home” near the plot.

  5. Background Color Coding:

    • Displays thresholds (if defined in the Threshold Manager) with a semi-transparent color scale for easy interpretation.
    • Each plot includes a header with the parameter name.

  6. Legend and Hover Details:

    • Threshold categories are displayed on hover.
    • Metadata group information and highlighted samples are also explained via hover tooltips.

  7. Download Options

    • The plot can be downloaded using the “camera” icon near the plot.
    • A single click allows users to download all plots together for reporting or documentation purposes.

Cluster plot navigation

The clustering plot is fully interactive via the following options:

  • hover over a sample point to display its information,
  • zoom using the mouse wheel,
  • pan by clicking and dragging, and
  • double-click on an empty area to reset the view.
  • Individual samples can be selected by clicking on points or legend entries; multiple samples can be selected using the lasso tool or by holding Shift to extend an existing selection.
  • Clicking on an empty area clears the selection.
  • The plot can be exported as an image using the Export Image button.