diff --git a/figures/MAM2EBRAINS/M2E_firing_rate.py b/figures/MAM2EBRAINS/M2E_firing_rate.py index c89214eab201aaccd8a6e35641db117de711d2be..e258df8f0c0552c8f27b5404abcafa0b4e2f8d4e 100644 --- a/figures/MAM2EBRAINS/M2E_firing_rate.py +++ b/figures/MAM2EBRAINS/M2E_firing_rate.py @@ -97,4 +97,5 @@ def plot_firing_rate_over_areas(M, data_path): ax.set_ylabel('Area', size=13) ax.set_xlabel('Time (ms)', size=13) - pl.colorbar(im) \ No newline at end of file + cbar = pl.colorbar(im) + cbar.set_label('spikes/s', fontsize=13) \ No newline at end of file diff --git a/figures/MAM2EBRAINS/M2E_visualize_fc.py b/figures/MAM2EBRAINS/M2E_visualize_fc.py index 749144ed1a5b08610f9c30d27dd481017b9a26fa..089f24f4747df2518d3a212d236efb8e2f659e46 100644 --- a/figures/MAM2EBRAINS/M2E_visualize_fc.py +++ b/figures/MAM2EBRAINS/M2E_visualize_fc.py @@ -99,13 +99,13 @@ def visualize_fc(M, data_path): """ Figure layout """ - fig = pl.figure(figsize=(10, 4)) + fig = pl.figure(figsize=(9, 4)) fig.suptitle('Simulated functional connectivity (left) and FC of macaque resting-state fMRI', - fontsize=17, x=0.5, y=1.1) + fontsize=17, x=0.53, y=1.15) axes = {} gs1 = gridspec.GridSpec(1, 2) gs1.update(left=0.05, right=0.95, top=1, - bottom=0, wspace=0.3, hspace=0) + bottom=0.3, wspace=0.3, hspace=0) axes['A'] = pl.subplot(gs1[:1, :1]) axes['B'] = pl.subplot(gs1[:1, 1:2]) @@ -188,9 +188,13 @@ def visualize_fc(M, data_path): ax = axes['B'] matrix_plot(M, ax, zero_diagonal(exp_FC), part_sim_index, 1., pos=(0, 0)) - + areas = np.array(M.area_list)[part_sim_index] area_string = areas[0] for area in areas[1:]: area_string += ' ' area_string += area + + pl.text(0.00, 0.15, r'Order of cortical areas:', transform=fig.transFigure, fontsize=13, fontweight='bold') + pl.text(0.00, 0.1, area_string, + transform=fig.transFigure, fontsize=11) diff --git a/figures/MAM2EBRAINS/M2E_visualize_time_ave_pop_rates.py b/figures/MAM2EBRAINS/M2E_visualize_time_ave_pop_rates.py index 973855e090c815a8425d6dae9bc86731e01baaee..a5845a7c1b05d1c25a186397050416b56ae991f6 100644 --- a/figures/MAM2EBRAINS/M2E_visualize_time_ave_pop_rates.py +++ b/figures/MAM2EBRAINS/M2E_visualize_time_ave_pop_rates.py @@ -67,7 +67,8 @@ def plot_time_averaged_population_rates(M, data_path, area_list=None, **keywords if masked_matrix.mask[i, j]: ax.text(j + 0.5, i + 0.5, 'X', va='center', ha='center', color='black', fontsize=23) - plt.colorbar(im) + cbar = plt.colorbar(im) + cbar.set_label('spikes/s', fontsize=13) if 'output' in keywords: plt.savefig(os.path.join(M.output_dir, '{}_rates.{}'.format(M.simulation.label, diff --git a/multi-area-model.ipynb b/multi-area-model.ipynb index 66da4f135b94d7fb3b6f49d59fa700ab292b62eb..b08687ce6932c9eeb460b91d0cfc7187941bb661 100644 --- a/multi-area-model.ipynb +++ b/multi-area-model.ipynb @@ -657,15 +657,6 @@ "Comparison of area-level functional connectivity (FC) between the down-scaled MAM and macaque experimental data. (A) Simulated FC measured by the zero-time-lag correlation coefficient of synaptic input currents. (B) FC of macaque resting-state fMRI (see Materials and methods)." ] }, - { - "cell_type": "markdown", - "id": "678741b2-6dfa-4f1d-b4d8-ccd84f104767", - "metadata": {}, - "source": [ - "**Order of cortical areas**: <br>\n", - "V1, V2, VP, V3, V3A, MT, V4t, V4, VOT, MSTd, PIP, PO, DP, MIP, MDP, VIP, LIP, PITv, PITd, MSTl, CITv, CITd, FEF, TF, AITv, FST, 7a, STPp, STPa, 46, AITd, TH" - ] - }, { "cell_type": "code", "execution_count": null,