run_name = 'p1d1w2f5s9to12a3_20170126_sdpol_comparison_ans';
%{
# Analyse Simulation file
- DEPENDENCIES:
- Requires 'p1d1w2f5s9to12r1_20170108_sdpol_comparison.m' to have run
- Project 1:
- Propofol PAC investigation
- Direction 1:
- Thalamus-only propofol PAC modeling
- Writing item 2:
- Journal article on results of p1d1
- Figure 5:
- Explanations of propofol GABA-A sustained alpha mechanisms, using
comparisons of baseline-silent depolarization & highdose-alpha, and
baseline-spindling & highdose-alpha. Includes extreme Tau_T and propofol
multiplier (spm) comparisons.
- Subfigures 9-12:
- Just the baseline-silent/depolarized and highdose-alpha cases for
comparison. Using more depolarized state 0.3, higher gh 0.0032
- Analysis 3:
- Just plotting silent/depolarized comparison plots like before. Now
removing ticklabels. Now restoring ticklabels to make FIG files for michelle
- Date Created:
- 20170126
- Inherits from:
- `p1d1q41c4i6a1_20160919_cOFF_propomech_f5_sdpol_ans.m`
%}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% 0. Figure specifications
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set all figure backgrounds to white
set(gcf,'color','w');
le_fontsize = 22;
le_linewidth = 1.5;
cornflowerblue = [0.4 0.6 0.92]; % because fight club
baseline_blue = [0 0 1];
tc_neuron = 2;
outgoing_dir = strcat('/projectnb/crc-nak/asoplata/dynasim_data/',...
run_name);
if exist(outgoing_dir,'dir') == 0
mkdir(outgoing_dir)
end
outgoing_plots_dir = strcat('/projectnb/crc-nak/asoplata/dynasim_data/',...
run_name, '/plots/');
if exist(outgoing_plots_dir,'dir') == 0
mkdir(outgoing_plots_dir)
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% 1. Load data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% - Note that run-data directory name is different from above run-analysis name
data_name = 'p1d1w2f5s9to12r1_20170108_sdpol_comparison';
data_dir = strcat('/projectnb/crc-nak/asoplata/dynasim_data/',...
data_name);
if ~exist('baseline','var')
baseline = load(strcat(data_dir, '/data/', 'study_sim1_data.mat'));
highdose = load(strcat(data_dir, '/data/', 'study_sim2_data.mat'));
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% 2. Plot relevant/interesting raw data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dt = 0.01;
downsample_factor = 6;
% Beginning of timespan we're interested in showing, in ms (after the initial
% condition transient)
timebegin = 1;
% End of timespan we're interested in showing, in ms
timelimit = 500;
timespan_indices = [round(timebegin/(dt*downsample_factor)):...
round(timelimit/(dt*downsample_factor))];
number_bins = 1000;
figno = 1;
% From 'p1d1q42c1i1to4a1_20160919_cOFF_f3_repro_all_ans':
% Judging from visual inspection, we can safely say the EFFECTIVE (as in, very
% high probability of leading to burst) T-current window of
% activation is limited to
tcurr_window.ceiling = -74;
tcurr_window.floor = -80;
% figno = figno + 1;
figure(figno)
plot(highdose(1).time(timespan_indices),...
highdose(1).TC_V(timespan_indices,tc_neuron),'r',...
'LineWidth',le_linewidth)
hold on
plot(baseline(1).time(timespan_indices),...
baseline(1).TC_V(timespan_indices,tc_neuron),...
'Color',baseline_blue,...
'LineWidth',le_linewidth)
% Add a transparent plane to illustrate the zoom
u = [timebegin; timebegin; timelimit; timelimit];
v = [tcurr_window.floor; tcurr_window.ceiling; tcurr_window.ceiling; tcurr_window.floor];
p = patch(u,v,'b','Marker','.','LineWidth',0.00001);
set(p,'FaceColor',cornflowerblue)
% Oldest version that does this transparency is 2014b...really. ugh MATLAB
set(p,'FaceAlpha',0.3)
% The only way to be REALLY SURE that it will actually increase the fontsize is
% to do it separately for EVERY axes object, AFTER everything's already been
% plotted
% I.e. Must change FontSize AFTER `plot()` has been called, since `plot()`
% "resets" the axes object...seriously I HATE MATLAB
% https://www.mathworks.com/matlabcentral/answers/131236-changing-fontsize-in-a-figure
set(gca,'FontSize',le_fontsize)
% set(gca,'XTickLabel','')
% set(gca,'YTickLabel','')
hold off
ylim([-90 60])
% title('TC#1 Voltage traces')
% ylabel('Voltage in mV')
saveas(gcf, strcat(outgoing_plots_dir, run_name, '_subfig', int2str(figno),...
'_vtrace.fig'))
figno = figno + 1;
figure(figno)
plot(baseline(1).time(timespan_indices),...
baseline(1).TC_V(timespan_indices,tc_neuron),...
'Color',baseline_blue,...
'LineWidth',le_linewidth)
hold on
plot(highdose(1).time(timespan_indices),...
highdose(1).TC_V(timespan_indices,tc_neuron),'r',...
'LineWidth',le_linewidth)
p = patch(u,v,'b','Marker','.','LineWidth',0.00001);
set(p,'FaceColor',cornflowerblue)
set(p,'FaceAlpha',0.3)
set(gca,'FontSize',le_fontsize)
% set(gca,'XTickLabel','')
% set(gca,'YTickLabel','')
hold off
ylim([-80 -60])
% title('Zoomed TC#1 Voltages')
% ylabel('Voltage in mV')
saveas(gcf, strcat(outgoing_plots_dir, run_name, '_subfig', int2str(figno),...
'_zoom_vtrace.fig'))
figno = figno + 1;
figure(figno)
plot(baseline(1).time(timespan_indices),...
baseline(1).TC_iTChing2010TC_hT(timespan_indices,tc_neuron),...
'Color',baseline_blue,...
'LineWidth',le_linewidth)
hold on
plot(highdose(1).time(timespan_indices),...
highdose(1).TC_iTChing2010TC_hT(timespan_indices,tc_neuron),'r',...
'LineWidth',le_linewidth)
set(gca,'FontSize',le_fontsize)
% set(gca,'XTickLabel','')
% set(gca,'YTickLabel','')
hold off
ylim([0 0.25])
% title('TC#1 T-current h_T')
% ylabel(sprintf('h_T (unitless)'))
saveas(gcf, strcat(outgoing_plots_dir, run_name, '_subfig', int2str(figno),...
'_h_T.fig'))
figno = figno + 1;
figure(figno)
plot(baseline(1).time(timespan_indices),...
baseline(1).TC_RE_iGABAAChing2010_IGABAAChing2010(timespan_indices,tc_neuron),...
'Color',baseline_blue,...
'LineWidth',le_linewidth)
hold on
plot(highdose(1).time(timespan_indices),...
highdose(1).TC_RE_iGABAAChing2010_IGABAAChing2010(timespan_indices,tc_neuron),'r',...
'LineWidth',le_linewidth)
set(gca,'FontSize',le_fontsize)
% set(gca,'XTickLabel','')
% set(gca,'YTickLabel','')
hold off
% title('RE->TC#1 I_{GABAA}')
% ylabel('I_{GABAA} in microA/cm^2')
saveas(gcf, strcat(outgoing_plots_dir, run_name, '_subfig', int2str(figno),...
'_I_GABAA.fig'))