dynamo.pl.exp_by_groups(adata, genes, layer=None, group=None, use_ratio=False, use_smoothed=True, log=True, angle=0, re_order=True, figsize=(4, 3), save_show_or_return='show', save_kwargs={})[source]

Plot the (labeled) expression values of genes across different groups (time points).

This function can be used as a sanity check about the labeled species to see whether they increase or decrease across time for a kinetic or degradation experiment, etc.

  • adata (AnnData) – an Annodata object

  • genes (list) – The list of genes that you want to plot the gene expression.

  • group (string (default: None)) – Which group information to plot aganist (as elements on x-axis). Default is None, or no groups will be used. Normally you should supply the column that indicates the time related to the labeling experiment. For example, it can be either the labeling time for a kinetic experiment or the chase time for a degradation experiment.

  • use_ratio (bool (default: False)) – Whether to plot the fraction of expression (for example NTR, new to total ratio) over groups.

  • use_smoothed (bool (default: ‘True’)) – Whether to use the smoothed data as gene expression.

  • log (bool (default: True)) – Whether to log1p transform the expression data.

  • angle (float (default: 0)) – The angle to rotate the xtick labels for the purpose of avoiding overlapping between text.

  • re_order (bool (default: True)) – Whether to reorder categories before drawing groups on the x-axis.

  • figsize (string (default: (4, 3))) – Figure size of each facet.

  • 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”: ‘exp_by_groups’, “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.


A violin plot that shows each gene’s expression (row) across different groups (time), produced by seaborn.