networkcommons.visual.plot_density

networkcommons.visual.plot_density(df, gene_ids, metadata=None, id_column='idx', sample_id_column='sample_ID', group_column='group', quantiles=[10, 90], title='Density Plot of Intensity Values', xlabel='Intensity', ylabel='Density')

Plots density of intensity values for specified genes, including mean and quantile lines, and separates distributions by groups if metadata is provided. Each gene is displayed in a separate subplot.

Parameters:

  • df (pd.DataFrame) – Input DataFrame containing gene data.

  • gene_ids (list of str) – List of specific genes to highlight.

  • metadata (pd.DataFrame) – Optional DataFrame containing metadata (sample_ID, group).

  • id_column (str) – Column name for identifying the gene.

  • sample_id_column (str) – Column name in metadata for sample IDs.

  • group_column (str) – Column name in metadata for groups.

  • quantiles (list of int) – List of quantiles to plot.

  • title (str) – Title of the plot.

  • xlabel (str) – Label for the x-axis.

  • ylabel (str) – Label for the y-axis.

Returns:

None