Interpreting the Jackstraw plot of Seurat
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21 months ago

I am having a hard time understanding the Jackstraw plot and how it is made. A discussion on GitHub here and on StackExchange here give some insights but I still have a few questions: enter image description here

  1. What does the axis of the Jackstraw plot represent. What is the meaning of Theoretical [runif(1000)] and empirical.
  2. What does the slope of the Jackstraw plot represents? What does each dot on that slope represent?
  3. Is there a detailed yet simplistic step by step explanation on how the P values are calculated starting from PCA loadings?
genomics seurat plot scrnaseq • 713 views

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