Clustering and Dimensionality Reduction¶
Clustering Trajectories¶
Trajectories can be clustered using traja.plotting.plot_clustermap()
.
Colors corresponding to each trajectory can be specified with the colors
argument.
- traja.plotting.plot_clustermap(displacements: List[Series], rule: Optional[str] = None, nr_steps=None, colors: Optional[List[Union[int, str]]] = None, **kwargs)[source]¶
Plot cluster map / dendrogram of trajectories with DatetimeIndex.
- Parameters
displacements – list of pd.Series, outputs of
traja.calc_displacement()
rule – how to resample series, eg ’30s’ for 30-seconds
nr_steps – select first N samples for clustering
colors – list of colors (eg, ‘b’,’r’) to map to each trajectory
kwargs – keyword arguments for
seaborn.clustermap()
- Returns
a
seaborn.matrix.ClusterGrid()
instance- Return type
cg
Note
Requires seaborn to be installed. Install it with ‘pip install seaborn’.
PCA¶
Prinicipal component analysis can be used to cluster trajectories based on grid cell occupancy.
PCA is computed by converting the trajectory to a trip grid (see traja.plotting.trip_grid()
) followed by PCA (sklearn.decomposition.PCA
).
- traja.plotting.plot_pca(trj: TrajaDataFrame, id_col: str = 'id', bins: tuple = (8, 8), three_dims: bool = False, ax=None)[source]¶
Plot PCA comparing animals ids by trip grids.
- Parameters
Trajectory (trj -) –
IDs (id_col - column representing animal) –
grid (bins - shape for binning trajectory into a trip) –
Default (three_dims - 3D plot.) – False (2D plot)
axes (ax - Matplotlib) –
- Returns
fig - Figure