spatialtis.plotting.expression_map#
- spatialtis.plotting.expression_map(data, rois, markers, use_shape=False, x_axis='marker', figsize=None, wspace=0, hspace=0.2, selected_types=None, cell_type_key=None, marker_key=None, shape_key=None, centroid_key=None, roi_key=None, **plot_options)[source]#
Visualize marker expression in ROI
- Parameters
- dataAnnData
The AnnData object for plotting.
- roislist of str
A list of ROI name that you want to plot.
- markerslist of str
A list of markers name that you want to plot.
- x_axis{‘marker’, ‘roi’}, default: ‘marker’
What is on the x-axis, the marker or roi.
- use_shapebool
Plot cell in polygon only when shape data is available.
- figsizetuple of float
The size of figure.
- wspacefloat, default: 0
The space between plots vertically.
- hspacefloat, default: 0.1
The space between plots horizontally.
- selected_typeslist of str
Select your interested cell types.
- cell_type_keystr, default:
Config.cell_type_key The column in .obs to store cell types.This will temporarily overwrite the global config.
- marker_keystr, default:
Config.marker_key The column in .var to store marker names.By default will read from the index of .var. This will temporarily overwrite the global config.
- shape_keystr, default:
Config.shape_key The column in .var to store cell shape in wkt format. This will temporarily overwrite the global config.
- centroid_keystr or list of str, default:
Config.centroid_key The column in .obs or .obsm to store centroid. This will temporarily overwrite the global config.
- roi_keystr, default:
Config.roi_key The columns in .obs that specific ROI.This will temporarily overwrite the global config.
- **plot_options
Pass to
milkviz.point_map()ormilkviz.polygon_map()