Heatmap by Sample — Sample-to-Sample Correlation

Header: Heatmap - Sample: Sample-to-Sample Correlation

This heatmap shows the Pearson correlation coefficient (based on VST — Variance Stabilising Transformation — values) between every pair of samples. It is a square matrix where both axes list the sample names, and each cell displays the correlation value.

The color scale ranges from -1 (blue, perfect anti-correlation) through 0 (white, no correlation) to 1 (deep red, perfect positive correlation). In a well-designed experiment, you should see high correlation (dark red) among biological replicates and within treatment groups.

This view is useful for quality control: it can reveal outlier samples, batch effects, or unexpected groupings.

The heatmap respects the Plot Width and Plot Height settings from the sidebar Appearance section. It will also scale up automatically when there are many samples (150 px per sample) to ensure labels and values remain readable, using whichever is larger — the sidebar setting or the sample-based size.

Correlation Matrix (Expandable)

Below the heatmap, an expandable Correlation Matrix table displays the exact Pearson r values for every sample pair.