networkcommons.visual.plot_rank

networkcommons.visual.plot_rank(df, bio_ids=None, figsize=(12, 6), x_label='Proteins', y_label='Average Intensity', title='Protein abundance Rank Plot', legend_labels=None, id_column='idx', average_color='blue', stdev_color='gray', stdev_alpha=0.2, highlight_color='red', highlight_size=5, highlight_zorder=5, filepath=None, render=False)

Plot a protein abundance rank plot.

This function generates a plot showing protein abundance ranked by their average intensity with an option to highlight specific proteins.

Return type:

Figure

Parameters:

dfpd.DataFrame

Input DataFrame containing gene or protein data.

bio_idslist of str, optional

List of specific genes or proteins to highlight. Defaults to None.

figsizetuple, optional

Size of the figure. Defaults to (12, 6).

x_labelstr, optional

Label for the x-axis. Defaults to ‘Proteins’.

y_labelstr, optional

Label for the y-axis. Defaults to ‘Average Intensity’.

titlestr, optional

Title of the plot. Defaults to ‘Protein abundance Rank Plot’.

legend_labelsdict, optional

Dictionary with legend labels for ‘average’, ‘stdev’, and ‘highlight’. Defaults to None.

id_columnstr, optional

Name of the column containing the IDs (e.g., gene symbols or proteins). Defaults to ‘idx’.

average_colorstr, optional

Color of the average intensity line. Defaults to ‘blue’.

stdev_colorstr, optional

Color of the standard deviation shaded area. Defaults to ‘gray’.

stdev_alphafloat, optional

Transparency for the standard deviation shaded area. Defaults to 0.2.

highlight_colorstr, optional

Color for highlighting specific genes or proteins. Defaults to ‘red’.

highlight_sizeint, optional

Size of the highlighted points. Defaults to 5.

highlight_zorderint, optional

Z-order for the highlighted points. Defaults to 5.

filepathstr, optional

Path to save the plot. If None, the plot will not be saved. Defaults to None.

renderbool, optional

Whether to display the plot. Defaults to False.

Returns:

matplotlib.figure.Figure

The figure object for the plot.