merquaco.figures.plot_every_z_plane

merquaco.figures.plot_every_z_plane(transcripts: DataFrame, subsample: int = 1000, rotation_degrees: int = -90, ms: float = 1, num_planes: int = 7, alpha: float = 0.5, color: str = 'black', title: str = '', out_file: str | Path = '', label_planes: bool = True)

Plots transcripts overview for each z plane in a row

Parameters:

  • transcripts (pd.DataFrame) – Transcripts table

  • subsample (int, optional) – Number to subsample transcripts by. Default is 1000

  • rotation_degrees (int, optional) – Degrees to rotate image by. Default is -90 to match vizualizer outputs

  • ms (float, optional) – Marker size for each transcript spot. Default is 1

  • num_planes (int, optional) – Number of z planes to plot. Default is 7.

  • alpha (float, optional) – Alpha parameter for plotting. Default is 0.5.

  • color (str, optional) – Color for plotting transcript spots. Default is ‘black’.

  • title (str, optional) – Title for plot. Default is ‘’.

  • out_file (str or Path, optional) – Path at which to save plot. Default is ‘’.

  • label_planes (bool, optional) – Whether to label z planes on figure. Default is False.

Returns:

ax – Modified axes object with plot

Return type:

matplotlib.Axes.axes