pyNBS.pyNBS_plotting.plot_cc_map

This function plots the co-clustering map, which is a visual representation of the outputs from the consensus_hclust_hard function. Examples of what the co-clustering map image looks like can be found in the example Jupyter notebooks described here.

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Function Call:

plot_cc_map(cc_table, linkage, row_color_map=None, col_color_map=None, verbose=True, **save_args)

Parameters:

• cc_hard_sim_table (required, pandas.DataFrame): The patient-by-patient co-clustering matrix. This is the cc_hard_sim_table output of the consensus_hclust_hard function. The co-clustering proportions in this matrix color the main grid of the co-clustering map.
• Z (required, numpy.ndarray): This is a linkage map of patients. This is the Z output of the consensus_hclust_hard function. This linkage map is used to construct the dendrogram on the top of the co-clustering map figure.
• row_color_map (optional, pandas.Series, default=None): A mapping of each patient/sample to an RGB color. If passed, this parameter will generate a color bar along the rows of the co-clustering map indicating by color which cluster each patient for the clustering defined by the name of the pandas Series. This color map can be generated by the cluster_color_assign function.
• col_color_map (optional, pandas.Series, default=None): A mapping of each patient/sample to an RGB color. If passed, this parameter will generate a color bar along the columns of the co-clustering map indicating by color which cluster each patient for the clustering defined by the name of the pandas Series. This color map can be generated by the cluster_color_assign function.
• verbose (optional, bool, default=True): Verbosity flag to indicate when the function is done running.
• **save_args (optional, dict, default=None): Dictionary of strings for saving results.
  • save_args['outdir']: A string containing the directory path of which to save the co-clustering map. If this parameter is given within **save_args, the function will automatically write the co-clustering map as a .png to this location.
  • save_args['job_name']: A string containing a file prefix for the co-clustering map saved in save_args['outdir']. Otherwise the base file name will default to cc_map.png. The job_name will also show up in the title of the plot.

Returns:

• None: This function does not return anything, it will only plot the co-clustering map and save it to file.

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Additional notes about this function:

This function is only currently produces .png files. Other image file extensions are not currently supported.