comments on Chapter 1, figure "Dynamic metrics of the cDBG during construction"

[ctb]

A few minor questions first -

• so, the sum of the n_ lines should equal one? and kmer_p always ends at x=1, y=1.
• if correct, would suggest adding 'proportion of nodes' as y axis label.
• might also make them a bit bigger so they take up the page width?

I think the discussion of this figure in the Results section is a good start, but I have lots of questions 😆 -

• yeast looks pretty different. this is because of high coverage?
• I still have some trouble understanding the dynamics after looking at this for a while. let's see -
  • n_circular should generally be small, ok
  • n_trivial isn't defined anywhere?
  • the kinks in kmer_p are from non-random sequencing, presumably? maybe verify this with shuffling?
  • wouldn't you expect a fair number of islands in RNAseq?
  • in yeast, it looks like n_islands is converging to a very different point than in the other two data sets; what gives?
  • maybe: if this is due to higher coverage, what happens if you subsample the yeast data set a whole bunch?
  • n_tips behavior is driven by error?

anyway, I think it would be very helpful to develop some intuition, maybe in another (simpler) figure.

also, a different or perhaps complementary tack - what interesting behavior is occurring in this figure that readers should be alerted to, and what behavior is just boring and "trivial"?

[ctb]

I see that you added some more discussion, will revisit.