stereo.plots.PlotCollection.spatial_scatter_by_gene

PlotCollection.spatial_scatter_by_gene(gene_name, dot_size=None, palette='CET_L4', color_bar_reverse=True, width=None, height=None, x_label='spatial1', y_label='spatial2', title=None, vmin=None, vmax=None, **kwargs)[source]

Draw the spatial distribution of expression quantity of the gene specified by gene names.

Parameters:

  • gene_name (Union[str, list, ndarray]) – a gene or a list of genes you want to show.

  • dot_size (Optional[int]) – the dot size, defaults to None.

  • palette (Optional[str]) – the color theme, defaults to 'CET_L4'.

  • color_bar_reverse (Optional[bool]) – if True, reverse the color bar, defaults to False

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

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

  • show_plotting_scale – wheter to display the plotting scale.

  • out_path – the path to save the figure.

  • out_dpi – the dpi when the figure is saved.

  • 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.

  • x_label (Optional[str]) – the x label.

  • y_label (Optional[str]) – the y label.

  • title (Optional[str]) – the title label.

  • vmin (Optional[float]) – The value representing the lower limit of the color scale. Values smaller than vmin are plotted with the same color as vmin.

  • vmax (Optional[float]) – The value representing the higher limit of the color scale. Values greater than vmax are plotted with the same color as vmax.