Chapter 7

Visualization

• Heatmap

  A heatmap is not a picture, it's a clustering algorithm plus a color choice, and both steps can quietly reverse your biology.

• PCA plot (scores plot)

  The plot that tells you in five seconds whether your experiment worked, or whether you're about to run differential expression on a batch effect.

• Volcano plot

  The one figure that decides which genes make it into your paper, so get the axis and the threshold right before you trust the shape.