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Clinical Data Analysis

Overview

The Clinical Data Analysis tool in the MMRF Virtual Lab allows researchers to generate interactive visualizations of key clinical attributes within a selected cohort. Users can explore demographic and diagnostic variables, create custom groupings, and visualize the data across multiple chart types.

These visualizations help researchers quickly identify trends and relationships in the clinical data, such as distributions by sex, race, or survival outcomes.

Accessing the Clinical Data Analysis Tool

To access this feature:

  1. Navigate to the Analysis Center from the main navigation bar.
  2. Select or create a cohort to analyze.
  3. Under Analysis Tools, click the Clinical Data Analysis card.

Clinical Data Analysis Center Overview

The page will display all available clinical attributes for your cohort along with interactive visualization options.

Key Features

The Clinical Data Analysis tool enables users to:

  • Select which clinical fields to display in the workspace.
  • View data distributions through histograms, box plots, and survival plots.
  • Create custom bins to re-group values for categorical or continuous variables.
  • Select subsets of data directly from a visualization to create new cohorts or modify existing ones.
  • Download visualizations as SVG or PNG images.
  • Export underlying data in JSON or TSV format.
  • Print all clinical variable cards and their active plots to a single PDF.

Enabling Clinical Variable Cards

Use the control panel on the left to choose which clinical variables to visualize. Click the toggle switches next to each variable to enable or disable its display. Each enabled variable appears as a card in the workspace with selectable plot types.

Clinical Data Analysis Variable Toggle

Clinical fields are grouped into the following categories:

  • Demographic: Patient characterization data (e.g., age, sex, race, ethnicity).
  • Diagnosis: Information on disease type, stage, and related diagnostic metrics.

Exploring Clinical Variable Visualizations

Each clinical variable card supports one or more visualization types. Use the icons in the upper-right corner of the card to switch between plot types.

Histogram

Displays the distribution of cases across a selected clinical field as a bar chart. This plot supports both categorical and continuous variables.

Features:

  • View frequency and percentage of cases in each category.
  • View the data in tabular format.
  • Select specific bars to define new cohorts or modify existing ones.
  • Download plots in SVG or PNG.
  • Export data in JSON or TSV formats.

Clinical Data Analysis Histogram

Survival Plot

Displays survival outcomes over time for one or more patient categories (e.g., gender or treatment type). The MMRF Virtual Lab uses the Kaplan–Meier estimator to calculate survival probability over time.

Required fields:

  • Days to death or days to last follow-up
  • Vital status (alive/deceased)
  • Category field to separate cases (e.g., gender or treatment group)

Features:

  • Select up to 5 categories to include in the plot.
  • View counts and survival percentages in the accompanying data table.
  • Download survival curves in SVG or PNG.
  • Export underlying data as JSON or TSV.

Clinical Data Analysis Survival Plot

Creating Custom Bins

Custom bins allow researchers to redefine how data are grouped within visualizations. You can apply this to both categorical and continuous variables.

Click Customize Bins → Edit Bins to open the configuration window.

Categorical Binning

  • Combine existing values into new, broader groups.
  • Rename or hide categories.
  • Ungroup or restore previously hidden values.

Clinical Data Analysis Categorical Binning

Continuous Binning

Two binning methods are supported:

1. Equidistant Bins

  • Define interval sizes (e.g., 10 years, 1,000 days).
  • Optionally set start and end values.

2. Custom Range Bins

  • Manually create bins with user-defined ranges.
  • Name each range and specify min/max values.

Clinical Data Analysis Continuous Binning Placeholder

You can reset any custom binning to default values at any time by selecting Reset to Default.

Exporting and Downloading

Each clinical card supports the following export options:

  • Download Visualization: Save as .svg or .png images for use in reports or presentations.
  • Download Data: Export the data table in .json or .tsv format.
  • Print to PDF: Generate a combined PDF containing all active clinical cards and plots.

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