spateo.plotting.interactive.agg#
Interactive plotting functions for aggregated UMI counts.
Module Contents#
Functions#
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Interactively display UMI density bins. |
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Display raw data within an AnnData with interactive polygon selection. |
- spateo.plotting.interactive.agg.contours(adata: anndata.AnnData, layer: str, colors: Optional[List] = None, scale: float = 0.05) plotly.graph_objects.Figure[source]#
Interactively display UMI density bins.
- Parameters
- adata
Anndata containing aggregated UMI counts.
- layer
Layer to display
- colors
List of colors.
- scale
Scale width and height by this amount.
- Returns
A Plotly figure
- spateo.plotting.interactive.agg.select_polygon(adata: anndata.AnnData, layer: str, out_layer: Optional[str] = None, ax: Optional[matplotlib.axes.Axes] = None, background: Optional[str] = None, **kwargs) matplotlib.widgets.PolygonSelector[source]#
Display raw data within an AnnData with interactive polygon selection.
- Parameters
- adata
Anndata containing aggregated UMI counts.
- layer
Layer to display. Defaults to X.
- out_layer
Layer to output selection result as a boolean mask. Defaults to {layer}_selection.
- ax
Axes to plot.
- background
string or None (optional, default ‘None`) The color of the background. Usually this will be either ‘white’ or ‘black’, but any color name will work. Ideally one wants to match this appropriately to the colors being used for points etc. This is one of the things that themes handle for you. Note that if theme is passed then this value will be overridden by the corresponding option of the theme.
- **kwargs
Additional keyword arguments are all passed to
spateo.pl.imshow().