Removing old viz modules

[wingedRuslan]

Documenting files that can be deleted after my PRs approved.

• scona/nilearn_plotting.py

  • graph_to_nilearn_array
  • plot_connectome_with_nilearn
  • view_connectome_with_nilearn
  • view_markers_with_nilearn

All these functions are implemented in PR #145.

• scona/make_figures.py

  • plot_anatomical_network
  • anatomical_layout

All these functions are Included in PR #140

• get_anatomical_layouts ! - Not
  " This code takes in a BrainNetwork that has x, y, z coordinates and integer node labels (0 to n-1) for n nodes and returns three dictionaries containing appropriate pairs of coordinates for sagittal, coronal and axial slices."

• view_corr_mat - Not

• scona/scripts/visualisation_commands.py

  • rescale - Not
  • view_corr_mat - Not

Have not worked on any of these functions. view_corr_mat seems to work fine, so I can easily (hopefully) refactor and include in another file that has all the visualizations. Or this function could be redesigned and use seaborn.heatmap.

• scona/scripts/make_figures.py - the one with 4000 lines

  • plot_rich_club
  • plot_degree_dist
  • plot_network_measures

Above 3 functions are included in PR #121

• add_colorbar - included in PR Implementation of anatomical network visualisations #140

• setup_color_list - included in PR Implementation of anatomical network visualisations #140

• plot_anatomical_network - included in PR Implementation of anatomical network visualisations #140

• plot_sagittal_network - seems like a special case of plot_anatomical_network ?

• pretty_scatter - Not
  "This function creates a scatter plot with a regression line for the y variable against the degrees of graph G"

• degree_r_values - Not

• create_violin_labels - Not
  "A little function to create a labels list for the MT depth violin plots"

• violin_mt_depths - Not

• violin_add_laminae - Not

• old_figure_1 - Not

• old_figure_2 - Not

• old_figure_3 - Not

• partial_volume_fig - Not

• all_mean_mt - Not

• nodal_ct_mt - Not

• get_von_economo_color_dict - Not

• get_von_economo_shapes_dict - Not

• von_economo_boxes - Not

• von_economo_scatter - Not

• add_four_hor_brains - Not

• add_cells_picture - Not

• figure_1 - Not

• figure_2 - Not

• figure_3 - Not

• figure_4 - Not

• calc_min_max - Not
  " Find min and max values such that all the data lies within 90% of the axis range"

• get_min_max_values - Not

• plot_circular_network - Not

• set_conn_types - Not

• rich_edges_nodes - Not

• results_matrix - Not

• figs_for_talk - Not

• network_summary_fig - Not

• mt_degree_network_fig - Not

• rescale - Not

• candidate_histogram - Not

• xyz_vs_measures - Not

• make_combo_matrix - Not

• make_combo_scatter - Not

• make_combo_figures - Not

• parcellation_4horbrains - Not

• mediation_figure - Not

As far as I understood the code inside this file you developed is especially for your paper. @KirstieJane if you wish to have smth in scona, let me know, and I will do that!

@KirstieJane what would you like to do with:

1. view_corr_mat
2. get_anatomical_layouts
3. rescale