Supplementary tables & assay design

[alimanfoo]

This PR has work on supplementary tables and assay design. Resolves #130.

[alimanfoo]

Apologies this is a bit of a behemoth. Now ready for review. Here's a summary of main changes...

• To get a consistent view on which haplotype group a haplotype belongs to, I've added some code to the artwork_networks notebook to write out a file with group membership.
• I've then modified the artwork_hapfreq_map notebook to use the network groups. This now properly accounts for haplotypes which carry a kdr allele but don't fall into one of the major haplotype groups, by adding a "other kdr" colour (black) to the pies and legend.
• I've then added a supp_tables notebook which generates all the supplementary data tables:
  • supp_table_variants_missense.csv - all non-synonymous variants, suggest this becomes Supplementary Table 1.
  • supp_table_variants_tracking.csv - variants for tracking haplotype groups, suggest this becomes Supplementary Table 2.
  • supp_table_variants_all.csv - variants to take into account when doing primer design, suggest this is Supplementary Table 3.
  • supp_table_haplotype_panel.csv - some meta-information about the haplotypes, including which group we put them in, suggest Supplementary Table 4.
  • There is also supp_table_haplotypes_tracking.csv which has the actual haplotypes for the tracking variants. Not sure if this is needed.
• Finally, there are some edits to main.tex, to consistify language, and also to tighten up the discussion on assay design.

Happy to discuss any aspect of course.

[cclarkson]

This all looks great, the tbl_variants_missense with all the isoforms is a particularly a great idea.

Just on thing caught my eye, and that was within the figure legend (line 398) wt is italicised where as later in the text (line 443) it isn't. Was that intentional?

[alimanfoo]

Thanks, no not intentional, was just being lazy, we should consistify. I thought italics looked a bit better and matched italicisation of "kdr", but happy to do either way. There's a couple of figures IIRC that would also need updating if we italicize everywhere.

On Thu, 3 May 2018, 12:46 Chris Clarkson, notifications@github.com wrote:

This all looks great, the tbl_variants_missense with all the isoforms is a particularly a great idea.

Just on thing caught my eye, and that was within the figure legend (line 398) wt is italicised where as later in the text (line 443) it isn't. Was that intentional?

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[alimanfoo]

Took the liberty of italicizing "wt" throughout text and figures.

[alimanfoo]

Hi @cclarkson, I just took a pass through the main text and have made some minor proofing edits. I saw this PR wasn't merged yet so took the liberty to push the changes here. I also realised that I had previously reordered the haplotype group colours in the map but hand't done the same in the EHH or haplotype length plots, so I have also reordered those for consistency.