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biofe merged 1 commit into from
May 31, 2026
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docs: fix macrostate counts and simulation time in plots.md captions #39

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23 changes: 12 additions & 11 deletions docs/plots.md
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Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,11 @@
MPP can generate 15 types of plots, all accessible through both the CLI (`-p <plot>`) and
the Python API (`mpp.plot.<method>(out)`).

Most examples use the HP35 villin headpiece dataset (35 residues, 12 macrostates,
`T none` lumping unless noted otherwise). The RMSD and Delta RMSD examples use the
PDZ3 dataset (`KL none`, 7 macrostates), which provides topology and trajectory
files required for those plots.
Most examples use the HP35 villin headpiece dataset (35 residues, 14 macrostates,
`T none` lumping unless noted otherwise) with a reduced test dataset. The
Chapman-Kolmogorov test example uses the full HP35 dataset (12 macrostates). The
RMSD and Delta RMSD examples use the PDZ3 dataset (`KL none`, 7 macrostates), which
provides topology and trajectory files required for those plots.

---

Expand All @@ -29,7 +30,7 @@ python -m MPP.run config.yml T none -Z Z.npy -p dendrogram -o dendrogram.pdf
mpp.plot.dendrogram("dendrogram.pdf")
```

**Example (HP35, `T none`, 12 macrostates):**
**Example (HP35, `T none`, 14 macrostates):**

![Dendrogram](assets/plots/dendrogram.png){ width=75% }

Expand Down Expand Up @@ -96,7 +97,7 @@ python -m MPP.run config.yml KL none -Z Z.npy -p sankey -o sankey.pdf
mpp.plot.sankey("sankey.pdf")
```

**Example (HP35, `KL none` vs `T none` reference, 14 vs 12 macrostates):**
**Example (HP35, `KL none` vs `T none` reference, 14 vs 14 macrostates):**

![Sankey diagram](assets/plots/sankey.png){ width=40% }

Expand Down Expand Up @@ -124,7 +125,7 @@ python -m MPP.run config.yml T none -Z Z.npy -p contacts -o contacts.pdf
mpp.plot.contact_rep("path/to/cluster_file", "contacts.pdf")
```

**Example (HP35, `T none`, 12 macrostates):**
**Example (HP35, `T none`, 14 macrostates):**

![Contact representation](assets/plots/contacts.png){ width=80% }

Expand All @@ -148,7 +149,7 @@ python -m MPP.run config.yml T none -Z Z.npy -p macrotraj -o macrotraj.pdf
mpp.plot.macrostate_trajectory("macrotraj.pdf")
```

**Example (HP35, `T none`, 12 macrostates, ~60 µs):**
**Example (HP35, `T none`, 14 macrostates, ~300 µs):**

![Macrostate trajectory](assets/plots/macrotraj.png){ width=100% }

Expand Down Expand Up @@ -253,7 +254,7 @@ python -m MPP.run config.yml T none -Z Z.npy -p state_network -o state_network.p
mpp.plot.state_network("state_network.pdf")
```

**Example (HP35, `T none`, 12 macrostates):**
**Example (HP35, `T none`, 14 macrostates):**

![State network](assets/plots/state_network.png){ width=100% }

Expand All @@ -278,7 +279,7 @@ python -m MPP.run config.yml T none -Z Z.npy -p transition_matrix -o tmat.pdf
mpp.plot.transition_matrix("tmat.pdf")
```

**Example (HP35, `T none`, 12 macrostates):**
**Example (HP35, `T none`, 14 macrostates):**

![Transition matrix](assets/plots/transition_matrix.png){ width=100% }

Expand All @@ -303,7 +304,7 @@ python -m MPP.run config.yml T none -Z Z.npy -p transition_time -o transition_ti
mpp.plot.transition_time("transition_time.pdf")
```

**Example (HP35, `T none`, 12 macrostates):**
**Example (HP35, `T none`, 14 macrostates):**

![Transition time](assets/plots/transition_time.png){ width=100% }

Expand Down
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