rnalysis.filtering.CountFilter.plot_expression

CountFilter.plot_expression(features: Union[List[str], str], samples: Union[GroupedColumns, Literal['all']] = 'all', count_unit: str = 'Normalized reads', split_plots: bool = False) Figure

Plot the average expression and standard error of the specified features under the specified conditions.

Parameters
  • features (str or list of strings) – the feature/features to plot expression for.

  • samples – A list of the sample names and/or grouped sample names to be plotted. All specified samples must be present in the CountFilter object. To average multiple replicates of the same condition, they can be grouped in an inner list. Example input: [[‘SAMPLE1A’, ‘SAMPLE1B’, ‘SAMPLE1C’], [‘SAMPLE2A’, ‘SAMPLE2B’, ‘SAMPLE2C’],’SAMPLE3’ , ‘SAMPLE6’]

  • count_unit (str, default 'Reads per million') – The unit of the count data. Will be displayed in the y axis.

  • split_plots (bool (default=False)) – if True, each gene will be plotted in its own Figure. Otherwise, all genes will be plotted in the same Figure.

_images/plot_expression.png

Example plot of plot_expression()