sc_toolbox.plot.gene_expression_dpt_ordered#

sc_toolbox.plot.gene_expression_dpt_ordered(data, genes, xlabel, order=3, conf_int=95, figsize=(12, 6), condition=None, label_size=15, cols=None, scale=None, ylim=None, save=None)[source]#

Plot smoothed expression of all cells ordered by pseudo time.

Parameters:

  • data – AnnData object

  • genes – List of genes for which individual line plots will be generated

  • xlabel – x-axis label

  • order – Order of x-axis labels from left to right

  • conf_int – Size of the confidence interval for the regression estimate

  • figsize (Tuple[int, int]) – Size of the figure as specified in matplotlib

  • condition – Split expression values by this grouping, one line per category will be drawn

  • label_size (int) – Size of the labels as specified in matplotlib

  • cols – List of colors to use for line plot

  • scale – Set to True to scale expression value to a range between 0 and 1

  • ylim – Upper limit on the y-axis if desired

  • save (Optional[str]) – Path to save the plot to

Example

../../_images/gene_expression_dpt_ordered.png
Example with columns:
../../_images/gene_expression_dpt_ordered_col.png