scona.wrappers package

Submodules

scona.wrappers.corrmat_from_regionalmeasures module

scona.wrappers.corrmat_from_regionalmeasures.corrmat_from_regionalmeasures(regional_measures_file, names_file, output_name, covars_file=None, method='pearson')

Read in regional measures, names and covariates files to compute correlation matrix and write it to output_name.

Parameters

• regional_measures_file (*) – a csv containing data for some regional measures with brain regions and covariates as columns and subjects as rows. The first row of regional_measures should be column headings.

• names_file (*) – a text file containing names of brain regions. One name per line of text. These names key columns in df to correlate over.

• covars_file (*) – a text file containing a list of covariates to account for. One covariate per line of text. These names key columns in df.

• output_name (*) – file name to save output matrix to.

scona.wrappers.corrmat_from_regionalmeasures.setup_argparser()

scona.wrappers.network_analysis_from_corrmat module

scona.wrappers.network_analysis_from_corrmat.network_analysis_from_corrmat(corr_mat_file, names_file, centroids_file, output_dir, cost=10, n_rand=1000, edge_swap_seed=None)

This is the big function! It reads in the correlation matrix, thresholds it at the given cost (incorporating a minimum spanning tree), creates a networkx graph, calculates global and nodal measures (including random comparisons for the global measures) and writes them out to csv files.

scona.wrappers.network_analysis_from_corrmat.setup_argparser()

Code to read in arguments from the command line Also allows you to change some settings

Module contents