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PSN diagnostic viz wishlist #52

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shraddhapai opened this issue Dec 18, 2017 · 0 comments
Open

PSN diagnostic viz wishlist #52

shraddhapai opened this issue Dec 18, 2017 · 0 comments

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@shraddhapai
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shraddhapai commented Dec 18, 2017

Wishlist for utilities to diagnose PSN-related troubles. Idea is for user to run these diagnostic tools to understand the effect of a particular similairty measure, whether it separates classes as intended, the effect of sparsification, and generally "are my networks capturing similarity the way I think they should"?

  • density plot of edge weight distribution (one net at a time)
  • plot PSN in cytoscape and apply a layout of interest (e.g. force-directed layout)
  • boxplot of edge weights for same/opposite classes
  • mutation nets: patient-gene checkerboard view , sorted by gene mutation rate
  • mutation nets: density plot of "pct cohort mutated" per gene
  • mutation nets: show patient-gene mutation overlaid on gene interaction network.
  • plot degree distribution for nets
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