Analyses: !SectionGrowth

SectionGrowth can be used to compare the growth of different groups of samples, e.g. wild type and domesticated or samples collected at different times, e.g. HPRC1 and HPRC2. Similar to the normal growth curve, this will be the average over all of the possible permutations, with the added requirement that in this case only permutations that respect the sections are taken into account. Similar to the growth calculation, this is done by exact calculation and not by sampling.

Example:

- !SectionGrowth
  sections: ./my_sections.tsv
  coverage: 1,1,2
  quorum: 0,0.1,0

sections: needs the path to a tsv file that contains all of the samples that should be part of the plot and the group they belong to. There can be as many groups as you want. The groups will appear in the plot in the order of first appearance in the tsv file. Example file:

GRCh38#0	HPRC1
HG00321#1	HPRC2
HG00321#2	HPRC2
HG00350#1	HPRC2
HG00350#2	HPRC2
HG00408#1	HPRC2
HG00408#2	HPRC2
HG00423#1	HPRC2
HG00423#2	HPRC2
HG00438#1	HPRC1
HG00438#2	HPRC1
HG00544#1	HPRC2
HG00544#2	HPRC2
HG02257#1	HPRC1
HG02257#2	HPRC1
HG02486#1	HPRC1
NA18982#2	HPRC2

(this file will result in HPRC1 being displayed first and HPRC2 second).

coverage and quorum behave identical to the way that is seen in Growth. Both are calculated over all of the sections.