rnalysis.filtering.CountFilter.box_plot

CountFilter.box_plot(samples: Union[GroupedColumns, Literal['all']] = 'all', notch: bool = True, scatter: bool = False, ylabel: str = 'log10(Normalized reads + 1)', title: Union[str, Literal['auto']] = 'auto', title_fontsize: float = 20, label_fontsize: float = 16, tick_fontsize: float = 12) → Figure

Generates a box plot of the specified samples in the CountFilter object in log10 scale. Can plot both single samples and average multiple replicates. It is recommended to use this function on normalized values and not on absolute read values. The box indicates 25% and 75% percentiles, and the white dot indicates the median.

Parameters

  • samples ('all' or list.) – 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’]

  • notch (bool (default=True)) – if True, adds a confidence-interval notch to the box-plot.

  • scatter (bool (default=False)) – if True, adds a scatter-plot on top of the box-plot.

  • ylabel (str (default='Log10(Normalized reads + 1)')) – the label of the Y axis.

  • title (str or 'auto' (default='auto')) – The title of the plot. If ‘auto’, a title will be generated automatically.

  • title_fontsize (float (default=30)) – determines the font size of the graph title.

  • label_fontsize (float (default=15) :param tick_fontsize: determines the font size of the X and Y tick labels.) – determines the font size of the X and Y axis labels.

Return type

a matplotlib Figure.

_images/box_plot.png

Example plot of box_plot(add_scatter=True)