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fix docs rendering problem
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@connor-french
connor-french committed Jun 26, 2024
1 parent 6aae605 commit 38762a7
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168 changes: 70 additions & 98 deletions docs/index.md
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Original file line number Diff line number Diff line change
Expand Up @@ -274,6 +274,8 @@ image, but the actual plot is interactive.
sp.plot_model(demo, r, 0)
```

<img src="images/plot_model.png" data-fig-align="center" />

### 4. Simulate genetic data

Before simulating this demography, we need to create a sample dictionary
Expand Down Expand Up @@ -306,57 +308,42 @@ This step may take a minute or so to run.
``` python
sim = sp.sim_ancestry(samples=sample_dict, demography=demo, sequence_length=1e5, record_provenance=False, random_seed=42)

sim
print(sim)
```

<div>
<style>
.tskit-table thead tr th {text-align: left;padding: 0.5em 0.5em;}
.tskit-table tbody tr td {padding: 0.5em 0.5em;}
.tskit-table tbody tr td:first-of-type {text-align: left;}
.tskit-details-label {vertical-align: top; padding-right:5px;}
.tskit-table-set {display: inline-flex;flex-wrap: wrap;margin: -12px 0 0 -12px;width: calc(100% + 12px);}
.tskit-table-set-table {margin: 12px 0 0 12px;}
details {display: inline-block;}
summary {cursor: pointer; outline: 0; display: list-item;}
</style>
<div class="tskit-table-set">
<div class="tskit-table-set-table">
&#10;
| <img
src="https://raw.githubusercontent.com/tskit-dev/administrative/main/tskit_logo.svg"
style="height: 32px;display: inline-block;padding: 3px 5px 3px 0;" /> <a
href="https://tskit.dev/tskit/docs/latest/python-api.html#the-treesequence-class"
target="_blank">Tree Sequence</a> | |
|--------------------------------------------------------------------------------------|-------------|
| Trees | 1 |
| Sequence Length | 100000.0 |
| Time Units | generations |
| Sample Nodes | 344 |
| Total Size | 205.8 KiB |
| Metadata | No Metadata |

</div>

<div class="tskit-table-set-table">

| Table | Rows | Size | Has Metadata |
|-------------|------|-----------|:------------:|
| Edges | 686 | 21.4 KiB | |
| Individuals | 172 | 4.7 KiB | |
| Migrations | 0 | 8 Bytes | |
| Mutations | 0 | 16 Bytes | |
| Nodes | 687 | 18.8 KiB | |
| Populations | 3481 | 155.4 KiB | ✅ |
| Provenances | 0 | 16 Bytes | |
| Sites | 0 | 16 Bytes | |

</div>

</div>
</div>
</div>
&#10;
╔═══════════════════════════╗
║TreeSequence ║
╠═══════════════╤═══════════╣
║Trees │ 1║
╟───────────────┼───────────╢
║Sequence Length│ 100000║
╟───────────────┼───────────╢
║Time Units │generations║
╟───────────────┼───────────╢
║Sample Nodes │ 344║
╟───────────────┼───────────╢
║Total Size │ 205.8 KiB║
╚═══════════════╧═══════════╝
╔═══════════╤════╤═════════╤════════════╗
║Table │Rows│Size │Has Metadata║
╠═══════════╪════╪═════════╪════════════╣
║Edges │ 686│ 21.4 KiB│ No║
╟───────────┼────┼─────────┼────────────╢
║Individuals│ 172│ 4.7 KiB│ No║
╟───────────┼────┼─────────┼────────────╢
║Migrations │ 0│ 8 Bytes│ No║
╟───────────┼────┼─────────┼────────────╢
║Mutations │ 0│ 16 Bytes│ No║
╟───────────┼────┼─────────┼────────────╢
║Nodes │ 687│ 18.8 KiB│ No║
╟───────────┼────┼─────────┼────────────╢
║Populations│3481│155.4 KiB│ Yes║
╟───────────┼────┼─────────┼────────────╢
║Provenances│ 0│ 16 Bytes│ No║
╟───────────┼────┼─────────┼────────────╢
║Sites │ 0│ 16 Bytes│ No║
╚═══════════╧════╧═════════╧════════════╝

We’ll take a peak at a single tree from the TreeSequence object to see
what it looks like. The `draw_tree()` function is a convenience function
that uses `msprime`’s `draw_text()` function to plot a single tree from
Expand Down Expand Up @@ -387,57 +374,42 @@ that the tree sequence has some mutations!
``` python
sim = sp.sim_mutations(sim, rate=1e-10, random_seed=490)

sim
print(sim)
```

<div>
<style>
.tskit-table thead tr th {text-align: left;padding: 0.5em 0.5em;}
.tskit-table tbody tr td {padding: 0.5em 0.5em;}
.tskit-table tbody tr td:first-of-type {text-align: left;}
.tskit-details-label {vertical-align: top; padding-right:5px;}
.tskit-table-set {display: inline-flex;flex-wrap: wrap;margin: -12px 0 0 -12px;width: calc(100% + 12px);}
.tskit-table-set-table {margin: 12px 0 0 12px;}
details {display: inline-block;}
summary {cursor: pointer; outline: 0; display: list-item;}
</style>
<div class="tskit-table-set">
<div class="tskit-table-set-table">
&#10;
| <img
src="https://raw.githubusercontent.com/tskit-dev/administrative/main/tskit_logo.svg"
style="height: 32px;display: inline-block;padding: 3px 5px 3px 0;" /> <a
href="https://tskit.dev/tskit/docs/latest/python-api.html#the-treesequence-class"
target="_blank">Tree Sequence</a> | |
|--------------------------------------------------------------------------------------|-------------|
| Trees | 1 |
| Sequence Length | 100000.0 |
| Time Units | generations |
| Sample Nodes | 344 |
| Total Size | 209.4 KiB |
| Metadata | No Metadata |

</div>

<div class="tskit-table-set-table">

| Table | Rows | Size | Has Metadata |
|-------------|------|-----------|:------------:|
| Edges | 686 | 21.4 KiB | |
| Individuals | 172 | 4.7 KiB | |
| Migrations | 0 | 8 Bytes | |
| Mutations | 48 | 1.8 KiB | |
| Nodes | 687 | 18.8 KiB | |
| Populations | 3481 | 155.4 KiB | ✅ |
| Provenances | 1 | 763 Bytes | |
| Sites | 48 | 1.2 KiB | |

</div>

</div>
</div>
</div>
&#10;
╔═══════════════════════════╗
║TreeSequence ║
╠═══════════════╤═══════════╣
║Trees │ 1║
╟───────────────┼───────────╢
║Sequence Length│ 100000║
╟───────────────┼───────────╢
║Time Units │generations║
╟───────────────┼───────────╢
║Sample Nodes │ 344║
╟───────────────┼───────────╢
║Total Size │ 209.4 KiB║
╚═══════════════╧═══════════╝
╔═══════════╤════╤═════════╤════════════╗
║Table │Rows│Size │Has Metadata║
╠═══════════╪════╪═════════╪════════════╣
║Edges │ 686│ 21.4 KiB│ No║
╟───────────┼────┼─────────┼────────────╢
║Individuals│ 172│ 4.7 KiB│ No║
╟───────────┼────┼─────────┼────────────╢
║Migrations │ 0│ 8 Bytes│ No║
╟───────────┼────┼─────────┼────────────╢
║Mutations │ 48│ 1.8 KiB│ No║
╟───────────┼────┼─────────┼────────────╢
║Nodes │ 687│ 18.8 KiB│ No║
╟───────────┼────┼─────────┼────────────╢
║Populations│3481│155.4 KiB│ Yes║
╟───────────┼────┼─────────┼────────────╢
║Provenances│ 1│763 Bytes│ No║
╟───────────┼────┼─────────┼────────────╢
║Sites │ 48│ 1.2 KiB│ No║
╚═══════════╧════╧═════════╧════════════╝

The mutations will be spread across the TreeSequence, but there are a
few on the first tree.

Expand Down
5 changes: 3 additions & 2 deletions docs/index.qmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -223,6 +223,7 @@ sp.plot_landscape(demo, r, 0, basemap=True)
sp.plot_model(demo, r, 0)
```

![](images/plot_model.png){fig-align="center"}

### 4. Simulate genetic data

Expand All @@ -245,7 +246,7 @@ This step may take a minute or so to run.
sim = sp.sim_ancestry(samples=sample_dict, demography=demo, sequence_length=1e5, record_provenance=False, random_seed=42)
sim
print(sim)
```


Expand All @@ -270,7 +271,7 @@ Overlaying mutations after simulating ancestry isn't necessary for calculating g
sim = sp.sim_mutations(sim, rate=1e-10, random_seed=490)
sim
print(sim)
```

The mutations will be spread across the TreeSequence, but there are a few on the first tree.
Expand Down

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