scispy.pl.plot_shape_along_axis

scispy.pl.plot_shape_along_axis#

scispy.pl.plot_shape_along_axis(sdata, group_lst=[], gene_lst=[], color_key='scmusk', sdata_group_key='scmusk', target_coordinates='global', palette=[], scale_expr=False, bin_size=50, rotation_angle=0, heatmap=False, save=False, figsize=(10, 6))#

Analyse cell types occurence and gene expression along x axis of a sdata polygon shape after an evenual rotation

Parameters:

  • sdata (SpatialData) – SpatialData object obtained by tl.get_sdata_polygon()

  • group_lst (tuple (default: [])) – group list to consider (related to label_obs_key)

  • gene_lst (tuple (default: [])) – gene list to consider

  • color_key (str (default: 'scmusk')) – label_key in sdata.table.obs to consider

  • sdata_group_key (str (default: 'scmusk')) – SpatialData element where to find the group label

  • target_coordinates (str (default: 'global')) – target_coordinates system of sdata object

  • scale_expr (bool (default: False)) – wether or not to scale the gene expression plot

  • bin_size (int (default: 50)) – size of bins for plotting (µm)

  • rotation_angle (int (default: 0)) – horary rotation angle of the shape before computing along x axis

  • save (bool (default: False)) – wether or not to save the figure

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