rnalysis.filtering.CountFilter.ma_plot

CountFilter.ma_plot(ref_column: Literal['auto'] | ColumnName = 'auto', columns: ColumnNames | Literal['all'] = 'all', split_plots: bool = False, title: str | Literal['auto'] = 'auto', title_fontsize: float = 20, label_fontsize: 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 β€˜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 β€˜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.