vignette! #48
vignette! #48
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| we've kept the individuals in a dict, so that for instance | ||
| `corners["topleft"]` is an array of all the individual IDs that are in the top left corner. | ||
| The IDs of the ancient individuals we will work with are kept in the array `ancient`. | ||
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Hey look you can make notes at specific locations. Like this one: here would be a good place to double-check that all the ancient samples are from a while ago, like:
for i in corners["ancient"]:
ind = ts.individual(i)
assert(ind.time >= 500 and ind.time < 520)
docs/vignette_space.rst
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| print(f"The tree sequence now has {ts.num_trees} trees," | ||
| f" and {ts.num_mutations} mutations.") | ||
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| Note since :meth:`mutate <msprime.mutate>` is an msprime method, it does not return a pyslim |
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Could use a `.. noteor.. warning`` block here to make this stand out.
docs/vignette_space.rst
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| We should check this: plot where these individuals lie | ||
| relative to everyone else. | ||
| The individuals locations are available in individual metadata, | ||
| but to make things easier, it's also present in a `num_individuals x 2` |
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I had a read through @petrelharp, looks excellent to me. This will really help people out. We've got to get VCF and metadata sorted out soon in tskit, the last bit really is unnecessarily awkward and confusing. |
omg, yes. |
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looks great - very helpful. It may be useful to add a note that the rates in recapitate( ) and mutate( ) are per-timestep and not per-generation. This is also relevant around line 230-235 where you discuss keeping SLiM mutations, because the rates in SLiM and the rates applied by mutate( ) will be in different units. Also very much yes on the VCF output. |
docs/vignette_space.rst
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| if ind_group[i] == "ancient" or ind_group[j] == "ancient": | ||
| pair_colors[k] = 1 | ||
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| fig = plt.figure(figsize=(6, 6)) |
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| fig = plt.figure(figsize=(6, 6)) | |
| fig = plt.figure(figsize=(6, 6),dpi=300) |
will make things a little prettier.
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This looks great and I think will be super useful, especially to me! Agreed that the last chunk is a little complicated, so that it'd be nice to have some of it taken care of by write_vcf(), but I recognize that that's complicated. Thanks for putting the vignette together, and feel free to close #47 as you see fit. |
Here's a draft of the answer to @gbradburd's nice suggestion in #47. It'd be great if some other folks could read this over and give suggestions or make edits. In particular,
Any input, @gbradburd, @bhaller, @cjbattey? To view the html version of this, you should be able to do
makein thedocs/directory.