lib5c.plotters.pca module

Module for plotting visualizations of the results of principle component analyses.

lib5c.plotters.pca.plot_multi_pca(proj, pcs=3, s=100, label_points=True, labels=None, levels=None, colors=None, hue_order=None, **kwargs)[source]

Create a multi-component grid of PCA plots.

Parameters

  • proj (np.ndarray) – The matrix of PCA-projected replicates.

  • pcs (int) – How many principle components should be plotted.

  • s (float) – The area of the points to plot on the scatterplot.

  • label_points (bool) – Pass True to annotate each point with its label.

  • labels (Optional[List[str]]) – String names identifying the replicates (the rows of proj). Pass None to simply label them with their row index within proj.

  • levels (Optional[Union[List[str], Dict[str, str]]]) – The “level” for each replicate. Can be passed as a list of string (matching the order of the rows of proj), or a dict mapping the labels to levels. Each “level” gets one color and one entry in the legend. If None is passed each replicate gets its own level (levels = labels).

  • colors (Optional[Dict[str, str]]) – Mapping from levels as strings to the color to use for that level. Pass None to use randomly assigned colors.

  • hue_order (Optional[List[str]]) – Pass a list of the level names to determine their order in the legend.

  • kwargs (kwargs) – Typical plotter kwargs.

Returns

The axis plotted on.

Return type

pyplot axis

Notes

If both log and scaled are True, the logarithm will be applied before scaling.

PCA will always mean-center the data.

lib5c.plotters.pca.plot_pca(proj, pcs=(0, 1), legend=True, s=100, label_points=True, labels=None, levels=None, colors=None, hue_order=None, **kwargs)[source]

Plots a PCA projection along two selected principal components.

Parameters

  • proj (np.ndarray) – The matrix of PCA-projected replicates.

  • pcs (Tuple[int]) – Which two (zero-indexed) principle components should be plotted.

  • legend (bool) – Pass True to include a legend.

  • s (float) – The area of the points to plot on the scatterplot.

  • label_points (bool) – Pass True to annotate each point with its label.

  • labels (Optional[List[str]]) – String names identifying the replicates (the rows of proj). Pass None to simply label them with their row index within proj.

  • levels (Optional[Union[List[str], Dict[str, str]]]) – The “level” for each replicate. Can be passed as a list of string (matching the order of the rows of proj), or a dict mapping the labels to levels. Each “level” gets one color and one entry in the legend. If None is passed each replicate gets its own level (levels = labels).

  • colors (Optional[Dict[str, str]]) – Mapping from levels as strings to the color to use for that level. Pass None to use randomly assigned colors.

  • hue_order (Optional[List[str]]) – Pass a list of the level names to determine their order in the legend.

  • kwargs (kwargs) – Typical plotter kwargs.

Returns

The axis plotted on.

Return type

pyplot axis