[ ] 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 #140
[ ] setup_color_list - included in PR #140
[ ] plot_anatomical_network - included in PR #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
Documenting files that can be deleted after my PRs approved.
[ ] scona/nilearn_plotting.py
graph_to_nilearn_arrayplot_connectome_with_nilearnview_connectome_with_nilearnview_markers_with_nilearnAll these functions are implemented in PR #145.
[ ] scona/make_figures.py
plot_anatomical_networkanatomical_layoutAll 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- Notrescale- Notview_corr_mat- NotHave not worked on any of these functions.
view_corr_matseems 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 useseaborn.heatmap.[ ] scona/scripts/make_figures.py - the one with 4000 lines
plot_rich_clubplot_degree_distplot_network_measuresAbove 3 functions are included in PR #121
[ ]
add_colorbar- included in PR #140[ ]
setup_color_list- included in PR #140[ ]
plot_anatomical_network- included in PR #140[ ]
plot_sagittal_network- seems like a special case ofplot_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- NotAs 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