scmags.ScMags.dot_plot

ScMags.dot_plot(cmap=<matplotlib.colors.LinearSegmentedColormap object>, figsize=(6, 14), log_transform=True, grid=False, plot_legends=True, plot_brackets=True, size_leg_title='Fraction of cells\\nin group (%)', col_leg_title='Mean expression\\nin group', wspace=0, largest_dot=90.0, smallest_dot=0.0, size_exponent=1.5, dot_edge_lw=1.2, dot_edge_color='k', legends_width=1.5, bracket_width=0.35, bracket_top_adj=-0.5, bracket_bot_adj=0.5, plot_name='scmags_dotplot', save_plot=False, plot_dpi=300)

This function draws the dot plot from the scanpy library In this plot,the colors represent the normalized within-cluster average expression, and the circles represent the within-cluster expression rates.

Parameters

  • cmap (Optional[str]) – Colormap for dotplot.

  • figsize (Optional[Tuple[int, int]]) – Figure size.

  • log_transform (bool) – Performs log normalization before finding in-cluster mean values.

  • grid (bool) – Draws grid.

  • plot_legends (bool) – Adds legends.

  • plot_legends – Adds brackets.

  • size_leg_title (Optional[str]) – Size legend title.

  • col_leg_title (Optional[str]) – Colorbar title.

  • wspace (Optional[float]) – The space between the legends and the main plot.

  • largest_dot (Optional[float]) – The size of the largest ring.

  • smallest_dot (Optional[float]) – The size of the smallest ring.

  • size_exponent (Optional[float]) – The exponential coefficient used for scaling expression rates.

  • dot_edge_lw (Optional[float]) – Thickness of the rings.

  • dot_edge_color (Optional[str]) – Color of the rings.

  • legends_width (Optional[float]) – Width of legends by figure.

  • bracket_width (Optional[float]) – Width of legends by figure.

  • bracket_top_adj (Optional[float]) – Adjustment that allows the brackets to slide up.

  • bracket_bot_adj (Optional[float]) – Adjustment that allows the brackets to slide down

  • plot_name (Optional[str]) – Name of plot to save

  • save_plot (bool) – If True, the plot is saved in the working directory.

  • plot_dpi (int) – The dpi value of the figure to be saved

Examples

>>> import scmags as mg
>>> li = mg.datasets.li()
>>> li.filter_genes()
>>> li.sel_clust_marker()
>>> li.dot_plot(figsize = (6,12), largest_dot = 200)
../_images/scmags-ScMags-dot_plot-1.png