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
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"?