bio_embeddings.visualize

Display t-SNE or UMAP projections from the project stage

bio_embeddings.visualize.render_3D_scatter_plotly(embeddings_dataframe: pandas.core.frame.DataFrame) → plotly.graph_objs._figure.Figure

Return a Plotly Figure (3D scatter plot) based on a DataFrame containing three components.

Parameters

embeddings_dataframe – the DataFrame must contain three numerical columns called component_0, component_1 and component_2. The DataFrame index will be used to identify the points in the scatter plot. Optionally, the DataFrame may contain a column called label which will be used to color the points in the scatter plot.

Returns

A 3D scatter plot

bio_embeddings.visualize.render_scatter_plotly(embeddings_dataframe: pandas.core.frame.DataFrame) → plotly.graph_objs._figure.Figure

Return a Plotly Figure (2D scatter plot) based on a DataFrame containing three components.

Parameters

embeddings_dataframe – the DataFrame must contain two numerical columns called component_0 and component_1. The DataFrame index will be used to identify the points in the scatter plot. Optionally, the DataFrame may contain a column called label which will be used to color the points in the scatter plot.

Returns

A 2D scatter plot

bio_embeddings.visualize.save_plotly_figure_to_html(figure: plotly.graph_objs._figure.Figure, path: str) → None

Store plotly figure as interactive HTML file

Parameters

• figure – A Plotly Figure

• path – A string representing the path and/or filename where the HTML figure should be stored (e.g.: /path/to/figure.html).