Correlation networks #256
Correlation networks #256
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hmmmm. not sure i added the thresholds used to the response yet.. |
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Looks generally good, but i have two larger comments
- Can you please explain the value of the extra BaseNetwork class? I don't follow why CorrelationNetwork can't just inherit from Network
- I'd like to voice my general disdain for functions with argument names "object" or "x" and are more than 4 lines long :) It makes the code so much harder to follow for me.
| linkColorScheme <- veupathUtils::matchArg(linkColorScheme) | ||
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| if (!inherits(isValidEdgeList(object), "logical")) { | ||
| stop(paste("Invalid edgeList:", isValidEdgeList(object), collapse = '\n')) |
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"edgeList" should be "linkList"? I think we're generally using "link" instead of edge, but i may be misremembering.
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this is gonna sound stupid, bc it is.. but for some reason i dont like the way linkList looks or sounds
Network has type
yea. it bothers me sometimes too.. unfortunately the arg/ docs i think have to keep saying 'object' or similar for the case of the S4 methods... but we could rapidly rename them within the methods maybe in the future.. |
in an effort to get to a place where we can filter our networks here based on correlation coef and pvalue, weve introduced some dedicated classes for networks specifically representing correlations.