diff --git a/docs/plots.md b/docs/plots.md index 54a622f..a96be16 100644 --- a/docs/plots.md +++ b/docs/plots.md @@ -3,10 +3,11 @@ MPP can generate 15 types of plots, all accessible through both the CLI (`-p `) and the Python API (`mpp.plot.(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. --- @@ -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% } @@ -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% } @@ -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% } @@ -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% } @@ -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% } @@ -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% } @@ -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% }