stereo.plots.PlotCollection.cells_plotting#

PlotCollection.cells_plotting(color_by='total_count', color_key=None, bgcolor='#2F2F4F', width=None, height=None, fg_alpha=0.5, base_image=None, base_im_to_gray=False)[source]#

Plot the cells.

Parameters:

  • color_by (Literal['total_count', 'n_genes_by_counts', 'gene', 'cluster']) – spcify the way of coloring, default to ‘total_count’. if set to ‘gene’, you need to specify a gene name by color_key. if set to ‘cluster’, you need to specify the key to get cluster result by color_key.

  • color_key (Optional[str]) – the key to get the data to color the plot, it is ignored when the color_by is set to ‘total_count’ or ‘n_genes_by_counts’.

  • bgcolor (Optional[str]) – set background color.

  • width (Optional[int]) – the figure width in pixels.

  • height (Optional[int]) – the figure height in pixels.

  • fg_alpha (Optional[float]) – the alpha of foreground image, between 0 and 1, defaults to 0.5 this is the colored image of the cells.

  • base_image (Optional[str]) – the path of the ssdna image after calibration, defaults to None it will be located behide the image of the cells.

  • reorganize_coordinate –

    if the data is merged from several slices, whether to reorganize the coordinates of the obs(cells), if set it to a number, like 2, the coordinates will be reorganized to 2 columns on coordinate system as below:

    data1 data2
    data3 data4
    data5 …
    … …

    if set it to False, the coordinates will not be changed.

  • horizontal_offset_additional – the additional offset between each slice on horizontal direction while reorganizing coordinates.

  • vertical_offset_additional – the additional offset between each slice on vertical direction while reorganizing coordinates.

Returns:

Cells distribution figure.