dynamo.pl.dynamics

dynamo.pl.dynamics(adata, vkey, 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 dropout, 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.

  • vkey (list of str) – key for variable or gene names.

  • unit (str (default: hour)) – The unit of the labeling time, for example, hours or minutes.

  • y_log_scale (bool (default: True)) – Whether or not to use log scale for y-axis.

  • ci (str (for example: “95%”) or None (default: None)) – The confidence interval to be drawed for the parameter fitting. Currently not used.

  • ncols (int or None (default: None)) – The number of columns in the plot.

  • figsize ([float, float] or (float, float) or None) – The size of the each panel in the figure.

  • dpi (float or None) – Figure resolution.

  • boxwidth (float) – The width of the box of the boxplot.

  • barwidth (float) – The width of the bar of the barplot.

  • true_param_prefix (str) – The prefix for the column names of true parameters in the .var attributes. Useful for the simulation data.

  • show_moms_fit (bool (default: True)) – Whether to show fitting curves associated with the stochastic models, only works for non-deterministic models.

  • show_variance (bool (default: True)) – Whether to add a boxplot to show the variance at each time point.

  • show_kin_parameters (bool (default: True)) – Whether to include the estimated kinetic parameter values on the plot.

  • gene_order (str (default: column)) – The order of genes to present on the figure, either row-major or column major.

  • font_size_scale (float (default: 1)) – A value that will be used for scaling

  • save_show_or_return ({‘show’, ‘save’, ‘return’} (default: show)) – Whether to save, show or return the figure.

  • save_kwargs (dict (default: {})) – A dictionary that will passed to the save_fig function. By default it is an empty dictionary and the save_fig 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.

Returns

Return type

Nothing but plot the figure of the metabolic fitting.