dynamo.pl.dynamics

dynamo.pl.dynamics(adata, genes, unit='hours', log_unnormalized=True, y_log_scale=False, ci=None, ncols=None, figsize=None, dpi=None, boxwidth=None, barwidth=None, true_param_prefix=None, show_moms_fit=False, show_variance=True, show_kin_parameters=True, gene_order='column', font_size_scale=1, save_show_or_return='show', save_kwargs={})[source]

Plot the data and fitting of different metabolic labeling experiments.

Note that if non-smoothed data was used for kinetic fitting, you often won’t see boxplot but only the triangles for the mean values. This is because the raw data has a lot of dropouts, thus the median is outside of the whiskers of the boxplot and the boxplot is then not drawn by default.

Parameters:

  • adata (AnnData) – an Annodata object.

  • genes (List[str]) – the key for variable or gene names.

  • unit (str) – the unit of the labeling time, for example, hours or minutes. Defaults to “hours”.

  • log_unnormalized (bool) – whether the data has logged value. Defaults to True.

  • y_log_scale (bool) – whether to use log scale for y-axis. Defaults to False.

  • ci (Optional[str]) – the confidence interval to be drawn for the parameter fitting. Currently not used. Defaults to None.

  • ncols (Optional[int]) – the number of columns in the plot. Defaults to None.

  • figsize (Union[List[float], Tuple[float, float], None]) – the size of the each panel in the figure. Defaults to None.

  • dpi (Optional[float]) – the resolution of the figure. Defaults to None.

  • boxwidth (Optional[float]) – the width of the box of the boxplot. Defaults to None.

  • barwidth (Optional[float]) – the width of the bar of the barplot. Defaults to None.

  • true_param_prefix (Optional[str]) – the prefix for the column names of true parameters in the .var attributes. Useful for the simulation data. Defaults to None.

  • show_moms_fit (bool) – whether to show fitting curves associated with the stochastic models, only works for non-deterministic models. Defaults to False.

  • show_variance (bool) – whether to add a boxplot to show the variance at each time point. Defaults to True.

  • show_kin_parameters (bool) – whether to include the estimated kinetic parameter values on the plot. Defaults to True.

  • gene_order (Literal['column', 'row']) – the order of genes to present on the figure, either row-major or column major. Defaults to “column”.

  • font_size_scale (float) – the scale factor of fonts. Defaults to 1.

  • save_show_or_return (Literal['save', 'show', 'return']) – whether to save, show or return the figure. Defaults to “show”.

  • save_kwargs (dict) –

    a dictionary that will be passed to the save_show_ret function. By default, it is an empty dictionary and the save_show_ret function will use the {

    ”path”: None, “prefix”: ‘dynamics’, “dpi”: None, “ext”: ‘pdf’, “transparent”: True, “close”: True, “verbose”: True

    } as its parameters. Otherwise, you can provide a dictionary that properly modify those keys according to your needs. Defaults to {}.

Raises:

ValueError – the gene specified does not have fitted kinetic parameters.

Return type:

Optional[Figure]

Returns:

None would be returned in default and the plotted metabolic fitting figure would be shown directly. If set save_show_or_return=’return’ as a kwarg, the axes of the plot would be returned.