rnalysis.filtering.CountFilter.ma_plot

CountFilter.ma_plot(ref_column: Union[Literal['auto'], ColumnName] = 'auto', columns: Union[ColumnNames, Literal['all']] = 'all', split_plots: bool = False, title: Union[str, Literal['auto']] = 'auto', title_fontsize: float = 20, label_fontsize: Union[float, Literal['auto']] = 'auto', tick_fontsize: float = 12) → List[Figure]

Generates M-A (log-ratio vs. log-intensity) plots for selected columns in the dataset. This plot is particularly useful for indicating whether a dataset is properly normalized.

Parameters

  • ref_column (name of a column or 'auto' (default='auto')) – the column to be used as reference for MA plot. If ‘auto’, then the reference column will be chosen automatically to be the column whose upper quartile is closest to the mean upper quartile.

  • columns (str or list of str) – A list of the column names to generate an MA plot for.

  • split_plots (bool (default=False)) – if True, each individual MA plot will be plotted in its own Figure. Otherwise, all MA plots will be plotted on the same Figure.

  • 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 list of matplotlib Figures.