spacipy.Stoarr.plot

Stoarr.plot(annotation=None, highlight=None, bg='black', highlight_bg='#808080', scalebar=True, dx=0.715, scalebar_length=500, alpha_shape=True, alpha=0.05, border=True, border_color='#000000', cmap=None, category=True, cbar=False, ax=None, outfile=None, vmin=None, vmax=None)

Imaging the object

Parameters:

  • annotation (pandas.DataFrame) – one column pandas DataFrame containing annotation, with object labels as index

  • highlight (list) – which value in the annotation table to highlight

  • highlight_bg (str) – hex code for the non-highlight values

  • bg (str) – background color

  • scalebar (bool, default True) – whether or not to plot the scale bar

  • dx (float) – pixel scale for scale bar calculation

  • scalebar_length (float) – length of the scale bar

  • alpha_shape (bool) – pass

  • alpha (float) – pass

  • border (bool, default True) – whether or not to plot the border for cell segment

  • border_color (str, default $000000) – cell border color

  • cmap (str, list) – color map used for plot, can be matplotlib colormap or hex code

  • category (bool, default True) – whether the value is category or continous type

  • cbar (bool, default False) – whether or not to plot the color bar

  • ax (matplotlib.Axis) – matplotlib.Axis

  • outfile (str) – save the image

  • vmin (int) – minimal and maximal value range for color

  • vmax (int) – minimal and maximal value range for color