stereo.plots.PlotCollection.violin#

PlotCollection.violin(keys=['n_genes_by_counts', 'pct_counts_mt', 'total_counts'], x_label='', y_label=None, show_stripplot=False, jitter=0.2, dot_size=0.8, log=False, rotation_angle=0, group_by=None, multi_panel=None, scale='width', ax=None, order=None, use_raw=False, palette=None, title=None)[source]#

Violin plot to show index distribution of quality control.

Parameters:

  • keys (Union[str, Sequence[str]]) – Keys for accessing variables of .cells.

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

  • y_label (Optional[list]) – y label.

  • show_stripplot (Optional[bool]) – whether to overlay a stripplot of specific percentage values.

  • jitter (Optional[float]) – adjust the dispersion of points.

  • dot_size (Optional[float]) – dot size.

  • log (Optional[bool]) – plot a graph on a logarithmic axis.

  • rotation_angle (Optional[int]) – rotation of xtick labels.

  • group_by (Optional[str]) – the key of the observation grouping to consider.

  • multi_panel (Optional[bool]) – Display keys in multiple panels also when groupby is not None.

  • scale (Literal['area', 'count', 'width']) – The method used to scale the width of each violin. If ‘width’ (the default), each violin will have the same width. If ‘area’, each violin will have the same area. If ‘count’, a violin’s width corresponds to the number of observations.

  • ax (Optional[Axes]) – a matplotlib axes object. only works if plotting a single component.

  • order (Optional[Iterable[str]]) – Order in which to show the categories.

  • use_raw (Optional[bool]) – Whether to use raw attribute of data. Defaults to True if .raw is present.

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

  • palette (Optional[str]) – color theme. For more color theme selection reference: https://seaborn.pydata.org/tutorial/color_palettes.html

  • out_path – the path to save the figure.

  • out_dpi – the dpi when the figure is saved.