% This is the code used to generate model figures for J Neurophys paper %
% % % % % % % % % % % % % % % % % Preliminary figures for nature paper % % % % % % %
% clear; load wrkspc.mat
addpath(genpath(fullfile('..','matlab_libdave1')))
addpath(fullfile('.','funcs_supporting'));
reload = 0; % % % % Reload .mat files
plot_phases = 0;
screen_phases=1; % If error in curve fitting too high, or amplitude too low, do not count.
plot_daynight_shift = 1; % Shifts x-axis on Fig1 and 2 to be from -6h to 18h; inserts black bar showing LD
linear_interp = 1;
if linear_interp % Use linear interpolation for sensitivity plot
linear_or_nearest='linear';
fiterr_thresh=33;
amperr_thresh=0.03;
else % Use nearest neighbour interpolation for sensplot
linear_or_nearest='nearest';
fiterr_thresh=10;
amperr_thresh=0.05;
end
fig_default=1;
fig0=1; % Raw traces
fig1=1; % Firing rates all3 phase shift
fig2=1; % Singles
fig2b=1; % Singles merged
fig3=1; % Sensitivity
fig4_suppl=1; % Supplementary senstitivity analysis
fig9=1;
fig_default=0;
fig0=0; % Raw traces. (Uses sim0; path_raw)
% fig1=0; % Used in J Neurophys paper for modeling figure. (Uses sim1; path_cutfimbria)
fig2=0; % Used for J Neurophys paper - Singles. (sim2; path_singles)
fig2b=0; % Singles merged; basket cells only I presume. Not used in J NEurophys, but maybe used in Conference paper?
fig3=0; % (Uses sim3 and sim4. Mainly sim4. Sim3 is sensitivity analysis, methinks. Sim4 corresponds to path_senschop.)
fig4_suppl=0;
fig9=0;
if (fig4_suppl); fig3=1; end
% Paper_figs.m
path_raw = '../output_paperdata'; % Default
name_raw = 'wrkspc_mode3_trimmed.mat';
% path_raw = '../../Tamas_CA1/04_saguaro/03_Schaffersyn/S3i_longsingle';
% name_raw = 'wrkspc_redo.mat';
path_cutfimbria = path_raw;
name_cutfimbria = 'wrkspc_mode3.mat';
% path_singles = '../../Tamas_CA1/04_saguaro/03_Schaffersyn/S3i_longsingle';
% name_singles = 'wrkspc_redo.mat';
path_singles = path_raw;
name_singles = 'wrkspc_mode5.mat';
% path_sens_m2b='../Tamas_CA1//04_saguaro/03_Schaffersyn/S3hsens_205';
% name_sens_m2b='wrkspc_full_clean';
path_senschop=path_raw;
name_senschop='wrkspc_mode4';
if ~(reload)
curr_dir = pwd;
cd (path_raw);
if ~exist('sim0','var');
load(name_raw);
sim0 = sim_crop;
end
cd (curr_dir);
curr_dir = pwd;
cd (path_cutfimbria);
if ~exist('sim1','var'); load(name_cutfimbria); sim1 = sim_clean; end
cd (curr_dir);
curr_dir = pwd;
cd (path_singles);
if ~exist('sim2','var'); load(name_singles); sim2 = sim_clean; end
cd (curr_dir);
% curr_dir = pwd;
% cd (path_sens_m2b);
% if ~exist('sim3','var'); load(name_sens_m2b); sim3 = sim_clean; end
% cd (curr_dir);
curr_dir = pwd;
cd (path_senschop);
if ~exist('sim4','var'); load(name_senschop); sim4 = sim_clean; end
cd (curr_dir);
end
font_scaling_def = 0.5;
linewidth_def=2;
markersize_def=10;
FS_axislabels_def=30;
FS_axis_def=30;
if fig_default
end
set_values_multi=0;
if fig0
font_scaling=0.5;
linewidth=linewidth_def;
markersize=markersize_def;
FS_axislabels=FS_axislabels_def*font_scaling;
FS_axis=FS_axis_def*font_scaling;
curr_dir = pwd;
cd (path_raw);
if reload; load (name_raw); else sim=sim0;end
cd (curr_dir);
figure1 = figure;
set (figure1, 'Position',[524 339 560*3/3 420*4/3]*font_scaling,'Color','w');
h4 = gca;
% set(h4,'OuterPosition',[0.1 0.0 0.9 1.0]);
% set(h4,'Position',[0.570340909090909 0.075185492801772 0.334659090909091 0.439]);
% leg1=legend('bc','msg','olm','pyr'); legend('boxoff'); set(leg1,'Position',[0.7244 0.6628 0.1252 0.264]);
% annotation(figure1,'textbox',[0.01 0.67 0.05455 0.08571],'String',{'bc'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels);
% annotation(figure1,'textbox',[0.01 0.52 0.05455 0.08571],'String',{'msg'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels);
% annotation(figure1,'textbox',[0.01 0.33 0.05455 0.08571],'String',{'olm'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels);
% annotation(figure1,'textbox',[0.01 0.17 0.05455 0.08571],'String',{'pyr'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels);
% annotation(figure1,'textbox',[0.4895 0.3129 0.05455 0.08571],'String',{'bc'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels);
% annotation(figure1,'textbox',[0.4895 0.2533 0.05455 0.08571],'String',{'msg'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels);
% annotation(figure1,'textbox',[0.4895 0.1776 0.05455 0.08571],'String',{'olm'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels);
% annotation(figure1,'textbox',[0.4895 0.1152 0.05455 0.08571],'String',{'pyr'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels);
% set(h2,'OuterPosition',[0.385 0 0.63 1.0]);
set_values=0
sim_num=1;
sim_num=sim_num+1;
cell_range=1:4;
time_range = (1:length(sim{sim_num}.time));
plot_on=0;
plot_traces = 1;
plot_inputs = 0;
plot_stats = ~plot_traces;
plot_error = 1;
plot_efield = 0;
if plot_efield; cell_range = 1:11; end
if plot_traces
cell_range=[1:4];
time_range=5;
dat_fieldname_sing='column.hist.ct';
datfield_t='column.hist.t';
dat_fieldname_sing='column.sptr.ct';
datfield_t='';
%%%%%% TO DO: Fix KAPPA - It gives non-intuitive values for pyr
%%% Are initial values biasing? Should I be chopping off some of the
%%% initial data points?
%%% Might also need to adjust bin size used by KAPPA.
end
cells_to_consider=[1]; % Number of cells of a given type to consider
% sim_num=1; sim_num=sim_num+1; % Varying SCN amp only; time=5 so everything is default
sim_num=1; sim_num=sim_num+1; % "Healthy case," time=5 (v close to default except EC input slightly off)
time_range=5;
plot_struct;
plotmat_arr=[];
plotmat_t_arr=[];
for i = 1:length(plotmat)
plotmat_arr = [plotmat_arr plotmat{i}(:,cells_to_consider)];
plotmat_t_arr = [plotmat_t_arr plotmat_t{i}(:)];
end
cell_types = [1 2 3 4]; % Types of cells to consider - we want only pyr, OLM, and msGABA
plotmat_arr = plotmat_arr(:,cell_types);
plotmat_t_arr = plotmat_t_arr(:,cell_types);
opt_struct.shift = -0.05;
for i = 1:size(plotmat_arr, 2); plotmat_arr(:,i) = plotmat_arr(:,i) + (i-1)*opt_struct.shift; end % Shift data upwards
% axes2 = axes('Parent',figure1,'Position',[0.4068 0.2286 0.2871 0.1857],...
% 'FontSize',12);
axes(h4);
opt_struct.shift = -0.1;
% plot_matrix(plotmat_t_arr, plotmat_arr,opt_struct,[],[],linewidth);
plot(plotmat_t_arr, plotmat_arr*1e3,'k','LineWidth',1);
xlabel('Time (sec)', 'FontSize',12);
ylabel('Vm (V)', 'FontSize',12);
set(gca, 'FontSize',12);
axis([0 3 -250 25])
ox=0.1; oy=-240; lenx=0.5; leny=20; % x is 0.50sec=500msec; y is 20 mV
plot_scale([(ox+lenx/2) oy], [1], [lenx],'k','sec','h')
plot_scale([ox (oy+leny/2)], [1], [leny],'k','mV','v')
set(h4,'Box','off');
set(h4,'Visible','off');
end
if fig1
font_scaling=font_scaling_def;
linewidth=linewidth_def;
markersize=markersize_def;
FS_axislabels=FS_axislabels_def*font_scaling;
FS_axis=FS_axis_def*font_scaling;
curr_dir = pwd;
cd (path_cutfimbria);
if reload; load(name_cutfimbria); else sim=sim1;end
cd (curr_dir);
set_values=0
sim_num=1;
sim_num=sim_num+1;
cell_range=1:4;
time_range = (1:length(sim{sim_num}.time));
plot_on=0;
plot_traces = 0;
plot_inputs = 0;
plot_stats = ~plot_traces;
plot_error = 1;
plot_efield = 0;
if plot_efield; cell_range = 1:11; end
if plot_traces
cell_range=[4];
time_range=8;
%%%%%% TO DO: Fix KAPPA - It gives non-intuitive values for pyr
%%% Are initial values biasing? Should I be chopping off some of the
%%% initial data points?
%%% Might also need to adjust bin size used by KAPPA.
end
cells_to_consider=[1 2 3 4];
sim_num=1; sim_num=sim_num+1;
plot_struct; pm1=plotmat_arr(:,cells_to_consider); pmz1=plotmat_zeitgeber_arr(:,cells_to_consider); pm_err1=plotmat_ste_arr(:,cells_to_consider);
sim_num=2; sim_num=sim_num+1;
plot_struct; pm2=plotmat_arr(:,cells_to_consider); pmz2=plotmat_zeitgeber_arr(:,cells_to_consider); pm_err2=plotmat_ste_arr(:,cells_to_consider);
% pm1(:,1) = pm1(:,1) * 25; pm1(:,2) = pm1(:,2) * 25; pm1(:,3) = pm1(:,3) * 25; pm1(:,4) = pm1(:,4) * 200;
% pm2(:,1) = pm2(:,1) * 25; pm2(:,2) = pm2(:,2) * 25; pm2(:,3) = pm2(:,3) * 25; pm2(:,4) = pm2(:,4) * 200;
% Plot both on a single graph
% figure;
% errorbar([pmz1 pmz2], [pm1 pm2], [pm_err1 pm_err2],':');
% hold on;errorbar([pmz1], [pm1], [pm_err1]);
pmz1 = [[pmz1-24];pmz1; [pmz1+24]];
pm1 = [pm1; pm1; pm1];
pm_err1 = [pm_err1; pm_err1; pm_err1];
pmz2 = [[pmz2-24];pmz2; [pmz2+24]];
pm2 = [pm2; pm2; pm2];
pm_err2 = [pm_err2; pm_err2; pm_err2];
index = find ((pmz1(:,1)>=0) .* (pmz1(:,1)<=36));
pm1=pm1(index,:); pmz1 = pmz1(index,:); pm_err1 = pm_err1(index,:);
index = find ((pmz2(:,1)>=0) .* (pmz2(:,1)<=36));
pm2=pm2(index,:); pmz2 = pmz2(index,:); pm_err2 = pm_err2(index,:);
%natureplot_for_hsp_plotyy
%natureplot_for_hsp_plot
figure1 = figure; set (figure1, 'Position',[524 339 560*3/3 420*4/3]*font_scaling,'Color','w');
h1=gca; errorbar([pmz1], [pm1], [pm_err1],'LineWidth',2);
figure1 = figure; set (figure1, 'Position',[524 339 560*3/3 420*4/3]*font_scaling,'Color','w');
h2=gca; errorbar([ pmz2], [ pm2], [ pm_err2],'LineWidth',2);
% set(h1,'OuterPosition',[0.00 0 0.4 1.0]);
% set(h2,'OuterPosition',[0.5 0 0.5 1.0]);
% annotation(figure1,'textbox',[0.07 0.92 0.05455 0.08571],'String',{'a'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
% annotation(figure1,'textbox',[0.49 0.92 0.05455 0.08571],'String',{'b'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
% annotation(figure1,'textbox',[0.07 0.44 0.05455 0.08571],'String',{'c'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
% annotation(figure1,'textbox',[0.49 0.44 0.05455 0.08571],'String',{'d'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
% title(['Plotting ' dat_fieldname_sing]);
axes(h1);
% xlabel('Time (hours)', 'FontSize',FS_axislabels);
% ylabel('Firing rate (s^{-1})', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 17]);
set(gca,'Box','off');
set(gca, 'FontSize',FS_axis);
if plot_daynight_shift
axis([-0 36 ylimits(1)-1 ylimits(2)+4]);
rectangle('Position',[-30 ylimits(1)-1 12 0.6],'FaceColor','k');
rectangle('Position',[-18 ylimits(1)-1 12 0.6],'FaceColor','w');
rectangle('Position',[-6 ylimits(1)-1 12 0.6],'FaceColor','k');
rectangle('Position',[6 ylimits(1)-1 12 0.6],'FaceColor','w');
rectangle('Position',[18 ylimits(1)-1 12 0.6],'FaceColor','k');
rectangle('Position',[30 ylimits(1)-1 12 0.6],'FaceColor','w');
end
xlim= get(gca,'XLim');
xtickarr = xlim(1):12:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
% % % Make all x-axis entries positive
xlabelarr = get(gca,'XTickLabel');
xlabelarr = str2num(xlabelarr);
% xlabelarr = xlabelarr + 24;
for ii = 1:length(xlabelarr)
if xlabelarr(ii) < 0;
xlabelarr(ii) = xlabelarr(ii) + 24;
end
end
set(gca,'XTickLabel',num2str(xlabelarr));
axes(h2);
% xlabel('Time (hours)', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 17]);
set(gca,'Box','off');
set(gca, 'FontSize',FS_axis);
leg1=legend('BC','MSG','O-LM','PYR');
legend('boxoff');
set (leg1,'FontSize',FS_axis);
pos = get(leg1,'Position');
set(leg1,'Position',[0.7317 0.7553 0.2289 0.2197]);
if plot_daynight_shift
axis([-0 36 ylimits(1)-1 ylimits(2)+4]);
rectangle('Position',[-30 ylimits(1)-1 12 0.6],'FaceColor','k');
rectangle('Position',[-18 ylimits(1)-1 12 0.6],'FaceColor','w');
rectangle('Position',[-6 ylimits(1)-1 12 0.6],'FaceColor','k');
rectangle('Position',[6 ylimits(1)-1 12 0.6],'FaceColor','w');
rectangle('Position',[18 ylimits(1)-1 12 0.6],'FaceColor','k');
rectangle('Position',[30 ylimits(1)-1 12 0.6],'FaceColor','w');
end
xlim= get(gca,'XLim');
xtickarr = xlim(1):12:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
% % % Make all x-axis entries positive
xlabelarr = get(gca,'XTickLabel');
xlabelarr = str2num(xlabelarr);
% xlabelarr = xlabelarr + 24;
for ii = 1:length(xlabelarr)
if xlabelarr(ii) < 0;
xlabelarr(ii) = xlabelarr(ii) + 24;
end
end
set(gca,'XTickLabel',num2str(xlabelarr));
if (1)
% h3 = axes('Parent',gcf,'Position',[0.2811 0.5818 0.1767 0.3768]);
% compass_arr(h3, real(Z_arr(1,:)),imag(Z_arr(1,:)));
end
plot_healthy_on = 1; natureplot_with_scalebars
plot_healthy_on = 0; natureplot_with_scalebars
end
if fig2
font_scaling=0.5;
linewidth=linewidth_def;
markersize=markersize_def;
FS_axislabels=FS_axislabels_def*font_scaling;
FS_axis=FS_axis_def*font_scaling;
curr_dir = pwd;
cd (path_singles);
if reload; load(name_singles); else sim=sim2;end
cd (curr_dir);
set_values=0;
sim_num=0;
sim_num=sim_num+1;
cell_range=1:4;
%time_range = (1:length(sim{sim_num}.time));
plot_on=0;
plot_traces = 0;
plot_inputs = 0;
plot_stats = ~plot_traces;
plot_error = 1;
plot_efield = 0;
if plot_efield; cell_range = 1:11; end
if plot_traces
cell_range=[4];
time_range=8;
%%%%%% TO DO: Fix KAPPA - It gives non-intuitive values for pyr
%%% Are initial values biasing? Should I be chopping off some of the
%%% initial data points?
%%% Might also need to adjust bin size used by KAPPA.
end
cells_to_consider=[1:4];
sim_num=0; sim_num=sim_num+1;
plot_struct; pm1=plotmat_arr(:,cells_to_consider); pmz1=plotmat_zeitgeber_arr(:,cells_to_consider); pm_err1=plotmat_ste_arr(:,cells_to_consider);
sim_num=1; sim_num=sim_num+1;
plot_struct; pm2=plotmat_arr(:,cells_to_consider); pmz2=plotmat_zeitgeber_arr(:,cells_to_consider); pm_err2=plotmat_ste_arr(:,cells_to_consider);
sim_num=2; sim_num=sim_num+1;
plot_struct; pm3=plotmat_arr(:,cells_to_consider); pmz3=plotmat_zeitgeber_arr(:,cells_to_consider); pm_err3=plotmat_ste_arr(:,cells_to_consider);
% figure;
% errorbar([pmz1 pmz2], [pm1 pm2], [pm_err1 pm_err2],':');
% hold on;errorbar([pmz1], [pm1], [pm_err1]);
% figure; errorbar([pmz1], [pm1], [pm_err1],'LineWidth',1);
% hold on; errorbar([ pmz2], [ pm2], [ pm_err2],':','LineWidth',2);
% hold on; errorbar([ pmz3], [ pm3], [ pm_err3],':','LineWidth',2);
% legend('b1','msg1','olm1','pyr1','b2','msg2','olm2','pyr2');
% title(['Plotting ' dat_fieldname_sing]);
% figure1 = figure;
% Plot phases!
if plot_phases
phi_arr=[]; A_arr=[]; perr_arr=[];
phi=[]; A=[]; perr=[];
for ii = cells_to_consider
[A(ii) phi(ii) mse_temp perr(ii)] = fit_sinwave(pmz1(:,ii), pm1(:,ii), 24);
end
phi_arr = [phi_arr; phi]; A_arr = [A_arr; A]; perr_arr = [perr_arr; perr];
phi=[]; A=[]; perr=[];
for ii = cells_to_consider
[A(ii) phi(ii) mse_temp perr(ii)] = fit_sinwave(pmz2(:,ii), pm2(:,ii), 24);
end
phi_arr = [phi_arr; phi]; A_arr = [A_arr; A]; perr_arr = [perr_arr; perr];
phi=[]; A=[]; perr=[];
for ii = cells_to_consider
[A(ii) phi(ii) mse_temp perr(ii)] = fit_sinwave(pmz3(:,ii), pm3(:,ii), 24);
end
phi_arr = [phi_arr; phi]; A_arr = [A_arr; A]; perr_arr = [perr_arr; perr];
mean_firing_rate = [mean(pm1); mean(pm2); mean(pm3)];
phi_arr_screened = phi_arr;
[rows cols] = size(phi_arr);
for ii = 1:rows
for jj = 1:cols
Cerr1=0;Cerr2=0;
if perr_arr(ii,jj) > fiterr_thresh; Cerr1 = 1; end
if mean_firing_rate(ii,jj)/A_arr(ii,jj) < amperr_thresh; Cerr2=1; end
if ((Cerr1 || Cerr2) && (screen_phases))
phi_arr_screened(ii,jj) = Inf;
end
end
end
figure1 = figure;
set (figure1, 'Position',[524 339 560 420],'Color','w');
phi_arr2 = phi_arr_screened;
phi_arr2 = fliplr(flipud(phi_arr2));
corder = get(0,'DefaultAxesColorOrder');
colormap (flipud(corder(1:size(phi_arr2,2),:)))
h_bar= barh(phi_arr2);
set (h_bar,'BaseValue',-6);
rectangle('Position',[-6 0.5 12 0.1],'FaceColor','k');
axis([-6 18 0.5 3.5]);
ylabelarr = {'Schaffer','Fimbria','mel'};
ylabelarr = fliplr (ylabelarr);
% set(gca,'YTick',1:length(ylabelarr))
set(gca,'YTickLabel',ylabelarr, 'FontSize', 10);
figure1 = figure;
set (figure1, 'Position',[524 339 560 420],'Color','w');
phi_arr2 = phi_arr_screened';
phi_arr2 = fliplr(flipud(phi_arr2));
h_bar= barh(phi_arr2);
set (h_bar,'BaseValue',-6);
rectangle('Position',[-6 0.5 12 0.1],'FaceColor','k');
axis([-6 18 0.5 4.5]);
ylabelarr = {'bc','msg','olm','pyr'};
ylabelarr = fliplr (ylabelarr);
% set(gca,'YTick',1:length(ylabelarr))
set(gca,'YTickLabel',ylabelarr, 'FontSize', 10);
end
if plot_daynight_shift
pmz1 = [[pmz1-24];pmz1; [pmz1+24]];
pm1 = [pm1; pm1; pm1];
pm_err1 = [pm_err1; pm_err1; pm_err1];
pmz2 = [[pmz2-24];pmz2; [pmz2+24]];
pm2 = [pm2; pm2; pm2];
pm_err2 = [pm_err2; pm_err2; pm_err2];
pmz3 = [[pmz3-24];pmz3; [pmz3+24]];
pm3 = [pm3; pm3; pm3];
pm_err3 = [pm_err3; pm_err3; pm_err3];
end
figure1 = figure;
set (figure1, 'Position',[524 339 560*3/3 420*4/3]*font_scaling,'Color','w');
% h1=subplot(111);
figure2 = figure;
set (figure2, 'Position',[524 339 560*3/3 420*4/3]*font_scaling,'Color','w');
% h2=subplot(111);
figure3 = figure;
set (figure3, 'Position',[524 339 560*3/3 420*4/3]*font_scaling,'Color','w');
% h3=subplot(111);
figure4 = figure;
set (figure4, 'Position',[524 339 560*3/3 420*4/3]*font_scaling,'Color','w');
% h4=subplot(111);
% yy=get(h1,'OuterPosition'); set(h1,'OuterPosition',[ yy(2) yy(3) yy(4)]);
% set(h2,'OuterPosition',[0.5 0 0.5 1.0]);
% annotation(figure1,'textbox',[0.03 0.92 0.05455 0.08571],'String',{'a'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
% annotation(figure1,'textbox',[0.48 0.92 0.05455 0.08571],'String',{'b'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
% annotation(figure1,'textbox',[0.03 0.45 0.05455 0.08571],'String',{'c'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
% annotation(figure1,'textbox',[0.48 0.45 0.05455 0.08571],'String',{'d'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
figure(figure2); errorbar([pmz1 ], [pm1 ], [pm_err1 ],'LineWidth',linewidth)
figure(figure3); errorbar([pmz2 ], [pm2 ], [pm_err2 ],'LineWidth',linewidth)
figure(figure4); errorbar([pmz3], [pm3], [pm_err3],'LineWidth',linewidth)
figure(figure2)
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([0 36 ylimits(1)-1 ylimits(2)+2.5]);
leg1=legend('BC','MSG','O-LM','PYR'); legend('boxoff'); set(leg1,'Position',[0.7494 0.7754 0.1869 0.1688]);
% xlabel('Time (hours)', 'FontSize',FS_axislabels);
% ylabel('Firing rate (s^{-1})', 'FontSize',FS_axislabels);
set(gca, 'FontSize',FS_axis,'Box','off');
rectangle('Position',[-30 ylimits(1)-1 12 0.4],'FaceColor','k');
rectangle('Position',[-18 ylimits(1)-1 12 0.4],'FaceColor','w');
rectangle('Position',[-6 ylimits(1)-1 12 0.4],'FaceColor','k');
rectangle('Position',[6 ylimits(1)-1 12 0.4],'FaceColor','w');
rectangle('Position',[18 ylimits(1)-1 12 0.4],'FaceColor','k');
rectangle('Position',[30 ylimits(1)-1 12 0.4],'FaceColor','w');
xlim= get(gca,'XLim');
xtickarr = xlim(1):12:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
figure(figure3)
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([0 36 ylimits(1)-1 ylimits(2)+1]);
% xlabel('Time (hours)', 'FontSize',FS_axislabels);
% ylabel('Firing rate (s^{-1})', 'FontSize',FS_axislabels);
set(gca, 'FontSize',FS_axis,'Box','off');
rectangle('Position',[-30 ylimits(1)-1 12 0.6],'FaceColor','k');
rectangle('Position',[-18 ylimits(1)-1 12 0.6],'FaceColor','w');
rectangle('Position',[-6 ylimits(1)-1 12 0.6],'FaceColor','k');
rectangle('Position',[6 ylimits(1)-1 12 0.6],'FaceColor','w');
rectangle('Position',[18 ylimits(1)-1 12 0.6],'FaceColor','k');
rectangle('Position',[30 ylimits(1)-1 12 0.6],'FaceColor','w');
xlim= get(gca,'XLim');
xtickarr = xlim(1):12:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
figure(figure4)
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([0 36 ylimits(1)-1 ylimits(2)+1]);
% xlabel('Time (hours)', 'FontSize',FS_axislabels);
% ylabel('Firing rate (s^{-1})', 'FontSize',FS_axislabels);
set(gca, 'FontSize',FS_axis,'Box','off');
rectangle('Position',[-30 ylimits(1)-1 12 0.4],'FaceColor','k');
rectangle('Position',[-18 ylimits(1)-1 12 0.4],'FaceColor','w');
rectangle('Position',[-6 ylimits(1)-1 12 0.4],'FaceColor','k');
rectangle('Position',[6 ylimits(1)-1 12 0.4],'FaceColor','w');
rectangle('Position',[18 ylimits(1)-1 12 0.4],'FaceColor','k');
rectangle('Position',[30 ylimits(1)-1 12 0.4],'FaceColor','w');
xlim= get(gca,'XLim');
xtickarr = xlim(1):12:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
curr_dir = pwd;
cd (path_cutfimbria);
if reload; load(name_cutfimbria); else sim=sim1;end
cd (curr_dir);
set_values=0;
sim_num=0;
sim_num=sim_num+1;
cell_range=1:4;
time_range = (1:length(sim{sim_num}.time));
plot_on=0;
plot_traces = 0;
plot_inputs = 1;
plot_stats = 0;
plot_error = 1;
plot_efield = 0;
if plot_efield; cell_range = 1:11; end
if plot_traces
cell_range=[4];
time_range=8;
%%%%%% TO DO: Fix KAPPA - It gives non-intuitive values for pyr
%%% Are initial values biasing? Should I be chopping off some of the
%%% initial data points?
%%% Might also need to adjust bin size used by KAPPA.
end
dat_fieldname_sing_arr = {'EC_val','SCN_val','mel_val'};
plot_struct
% axes3 = axes('Parent',figure1,'Position',[0.3982 0.21 0.2518 0.259],...
% 'FontSize',12);
pmz4 = plotmat_zeitgeber_arr;
pm4 = plotmat_arr;
pmz4 = [[pmz4-24];pmz4; [pmz4+24]];
pm4 = [pm4; pm4; pm4];
%pm_err4 = [pm_err4; pm_err4; pm_err4];
figure(figure1); hold on;
corder = jet(10);
corder = corder(floor(linspace(length(corder)/3,length(corder)/1.0,3)),:);
corder = [ 0.0 0.6666 1.0;
0.3333 1.0000 0.6667;
1.0000 0.3333 0];
set(gca,'ColorOrder',corder);
plot(pmz4,pm4,'LineWidth',linewidth);
% plot(plotmat_zeitgeber_arr(:,1),plotmat_arr(:,1),'LineWidth',linewidth,'Color',[1 1 1]*0);
% plot(plotmat_zeitgeber_arr(:,2),plotmat_arr(:,2),'LineWidth',linewidth,'Color',[1 1 1]*0.5);
% plot(plotmat_zeitgeber_arr(:,3),plotmat_arr(:,3),'LineWidth',linewidth,'Color',[1 1 1]*0.7);
% legend(dat_fieldname_sing_arr, 'FontSize',12);
% xlabel('Time (hours)', 'FontSize',12);
% ylabel('Firing rate (s^{-1})', 'FontSize',12);
% set(gca, 'FontSize',12);
% ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
% axis([-2 24 ylimits(1) ylimits(2)]);
figure(figure1)
leg1=legend({'CA3 PYR','MSG','GABA_A'}); legend('boxoff'); %set(leg1,'Position',[0.7244 0.6628 0.1252 0.264]);
%set(leg1,'Position',[0.286 0.8304 0.1869 0.1688]);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([0 36 ylimits(1)-0.1 ylimits(2)+0.25]);
% xlabel('Time (hours)', 'FontSize',FS_axislabels);
% ylabel('Scaling factor', 'FontSize',FS_axislabels);
set(gca, 'FontSize',FS_axis,'Box','off');
set(gcf,'DefaultAxesColorOrder',[0 0 0;0.1 0.1 0.1;0.2 0.2 0.2])
rectangle('Position',[-30 ylimits(1)-0.1 12 0.03],'FaceColor','k');
rectangle('Position',[-18 ylimits(1)-0.1 12 0.03],'FaceColor','w');
rectangle('Position',[-6 ylimits(1)-0.1 12 0.03],'FaceColor','k');
rectangle('Position',[6 ylimits(1)-0.1 12 0.03],'FaceColor','w');
rectangle('Position',[18 ylimits(1)-0.1 12 0.03],'FaceColor','k');
rectangle('Position',[30 ylimits(1)-0.1 12 0.03],'FaceColor','w');
xlim= get(gca,'XLim');
xtickarr = xlim(1):12:24;
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
plot_singles_num = 1; natureplot_singles_scalebars;
plot_singles_num = 2; natureplot_singles_scalebars;
plot_singles_num = 3; natureplot_singles_scalebars;
end
if fig2b
figure1 = figure;
set (figure1, 'Position',[524 339 560*3/3 420*4/3]*font_scaling,'Color','w');
h2 = gca;
merg_pmz = [pmz1(:,1) pmz2(:,1) pmz3(:,1)];
merg_pm = [pm1(:,1) pm2(:,1) pm3(:,1)];
merg_pmerr = [pm_err1(:,1) pm_err2(:,1) pm_err3(:,1)];
corder = jet(10);
corder = corder(floor(linspace(length(corder)/3,length(corder)/1.0,3)),:);
set(gca,'ColorOrder',corder);
hold on; plot([merg_pmz], [merg_pm],'LineWidth',linewidth)
% hold on; errorbar([merg_pmz], [merg_pm], [merg_pmerr],'LineWidth',linewidth)
axes(h2);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-0 36 ylimits(1)-1 ylimits(2)+2]);
leg1=legend({'Schaffer','septal','mel'}); legend('boxoff');
% xlabel('Time (hours)', 'FontSize',FS_axislabels);
% ylabel('Firing rate (s^{-1})', 'FontSize',FS_axislabels);
set(gca, 'FontSize',FS_axis,'Box','off');
rectangle('Position',[-30 ylimits(1)-1 12 0.3],'FaceColor','k');
rectangle('Position',[-18 ylimits(1)-1 12 0.3],'FaceColor','w');
rectangle('Position',[-6 ylimits(1)-1 12 0.3],'FaceColor','k');
rectangle('Position',[6 ylimits(1)-1 12 0.3],'FaceColor','w');
rectangle('Position',[18 ylimits(1)-1 12 0.3],'FaceColor','k');
rectangle('Position',[30 ylimits(1)-1 12 0.3],'FaceColor','w');
xlim= get(gca,'XLim');
xtickarr = xlim(1):12:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
end
if fig3
font_scaling=1.0;
linewidth=linewidth_def;
markersize=markersize_def;
FS_axislabels=FS_axislabels_def*font_scaling;
FS_axis=FS_axis_def*font_scaling;
set_values_multi=0;
% % % % % Set up stuff for multi_plot
sim_start=0;
plot_summary=0; % Turns plots containing data from multiple simulations
plot_2D_sens = 1;
if plot_2D_sens;
cell_to_plot = 1; % 1 for basket cells
error_threshold = 50;
uniform_row = 0; % Make bottom row(s) of plot uniform
rownum = 1;
show_sensplot = 0;
use_colourmap = 0;
end
plot_across_experiments = 1; % Plot a single cell across multiple experimnets (different colour code per exp).
plot_across_cells = ~plot_across_experiments; % Plot all cells across multiple experiments
cell2plot = 1; % Cell number to use for 2D plots and for plotting across experiments
new_legarr = {'basket','msg','olm','pyr'};
fignum=88 + sim_start + plot_across_experiments*2;
% % % % Sim3 - Vary MSG 2 B divergence
% sim = sim3;
% loop1ROI=[3]; loop1range = 1:6; % Range of interest for outer loop; Total number of iterations of outer loop
% loop2ROI=[1 6]; loop2range = 1:8; % Range of interest for inner loop; Total number of iterations of inner loop
% experiment_ROI = [0]; experiment_range = 0:0; % Experiment number of interest within loops; Total number of experiments within nested loops
% if plot_2D_sens
% loop1ROI = loop1range; loop2ROI = loop2range(2:8); % If doing sensitivity analysis, need to use whole grid.
% end
% loop1vals = [-0.04 -0.08 -0.12 -0.16 -0.20 -0.24]; % We absolute value these later ...just incase
% loop2vals = [0 4 8 12 16 20 24 28]; % We absolute value these later ...just incase
% multi_plot;
% C_phi_interp1 = C_phi_interp;
% C_err_interp1 = C_err_interp;
% x1=x; y1=y;
%
% pm_zeit_cell1 = pm_zeit_cell;
% pm_cell1 = pm_cell;
% pm_ste_cell1 = pm_ste_cell;
% bC_phi1 = reshape(C_phi,1,length(C_phi(:)));
% bC_err1 = reshape(C_err,1,length(C_err(:)));
% % % % Sim4 - Vary strength of fimbria input
sim = sim4;
loop1ROI=[6]; loop1range = [1:7]; % Range of interest for outer loop; Total number of iterations of outer loop
loop2ROI=[2:5]; loop2range = 1:7; % Range of interest for inner loop; Total number of iterations of inner loop
experiment_ROI = [0]; experiment_range = 0:0; % Experiment number of interest within loops; Total number of experiments within nested loops
if plot_2D_sens
loop1ROI = loop1range([1:7]); loop2ROI = loop2range([1:7]); % If doing sensitivity analysis, need to use whole grid.
% Note, for this simulation, sim{36:38} have bad values (sim
% terminated on error)
end
loop1vals = [-0.05 -0.075 -0.085 -0.10 -0.12 -0.14 -0.18]; % We absolute value these later ...just incase
loop2vals = [0.0 0.15 0.3 0.45 0.65 0.80 1.0]*50; % We absolute value these later ...just incase
multi_plot;
C_phi_interp2 = C_phi_interp;
C_err_interp2 = C_err_interp;
x2=x; y2=y;
pm_zeit_cell2 = pm_zeit_cell;
pm_cell2 = pm_cell;
pm_ste_cell2 = pm_ste_cell;
bC_phi2 = reshape(C_phi,1,length(C_phi(:)));
bC_err2 = reshape(C_err,1,length(C_err(:)));
figure1 = figure;
set (figure1, 'Position',[524 339 560*3/2 420]*font_scaling,'Color','w');
annotation(figure1,'textbox',[0.03 0.92 0.05455 0.08571],'String',{'a'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
annotation(figure1,'textbox',[0.47 0.92 0.05455 0.08571],'String',{'b'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
h1 = subplot(121);
% imagesc(x1,y1,C_phi_interp1,[0 12]); set(gca,'YDir','normal')
% %colorbar;
% h = findall(gca,'Type','image');
% set (h(1), 'AlphaData',1-C_err_interp1); % Set transparency to account for error.
% xlabel('Mel amp', 'FontSize',FS_axislabels);
% ylabel('msg to bc divergence', 'FontSize',FS_axislabels);
% %title('Peak firing (hours)', 'FontSize',FS_axislabels);
% hold on;
% plot(0.12,20,'kx','MarkerSize',markersize,'LineWidth',2)
% plot([0.12 0.12],[0 28],'k:','LineWidth',1)
% plot([0.0 0.24],[20 20],'k:','LineWidth',1)
h2 = subplot(122);
xlabel('Mel amp', 'FontSize',FS_axislabels);
imagesc(x2,y2*100/50,C_phi_interp2,[0 12]); set(gca,'YDir','normal')
set(gca, 'FontSize',FS_axis/3*2);
% imagesc(x2,y2*4,C_phi_interp2,[0 12]); set(gca,'YDir','normal')
h = findall(gca,'Type','image');
set (h(1), 'AlphaData',1-C_err_interp2); % Set transparency to account for error.
xlabel('Mel amp', 'FontSize',FS_axislabels);
ylabel(['Septal innervation (% max)'], 'FontSize',FS_axislabels);
hcb = colorbar;
hcb2 = get(hcb,'Title');
set(hcb2,'String','Basket peak firing T_0 (hours)','Position',[4,6,1.005],'Rotation',270,'FontSize',FS_axislabels)
hold on;
plot(0.12,100,'kx','MarkerSize',markersize,'LineWidth',2)
plot(0.12,0,'kx','MarkerSize',markersize,'LineWidth',2)
plot([0.12 0.12],[0 160],'k:','LineWidth',1)
plot([0.0 0.24],[100 100],'k:','LineWidth',1)
set (h1,'Position',[0.08929 0.1333 0.3395 0.7929]);
set (h2,'Position',[0.5703 0.1333 0.3395 0.7929]);
% h_ann = annotation(figure1,'textbox',[0.03 0.92 0.05455 0.08571],'String',{'Peak firing (hours)'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels);
% h3 = axes('YAxisLocation','right','Color','none');
% set (h3,'Position',[0.9012 0.2881 0.008333 0.5557]);
% h_ylabel = ylabel ('Peak firing (hours)','FontSize',FS_axislabels);
% set(h3,'Box','off');
% set(h3,'Visible','off');
% set(h_ylabel,'Visible','on','Rotation',270);
if use_colourmap
figure;
cmap = colormap;
ncodes = size(colormap,1);
Cphi_rgb = ind2rgb(wcodemat(C_phi,ncodes,'mat'), cmap);
for ii = 1:size(C_err,1);
for jj = 1:size(C_err,2);
if (C_err(ii,jj))
Cphi_rgb(ii,jj,1) = 1.0;
Cphi_rgb(ii,jj,2) = 1.0;
Cphi_rgb(ii,jj,3) = 1.0;
end
end
end
image(x,y,Cphi_rgb); set(gca,'YDir','normal');
Cphi_rgb_int(:,:,1) = interp2(xvals, yvals, Cphi_rgb(:,:,1),loop1vals_interp,loop2vals_interp,'linear');
Cphi_rgb_int(:,:,2) = interp2(xvals, yvals, Cphi_rgb(:,:,2),loop1vals_interp,loop2vals_interp,'linear');
Cphi_rgb_int(:,:,3) = interp2(xvals, yvals, Cphi_rgb(:,:,3),loop1vals_interp,loop2vals_interp,'linear');
figure; image(x,y,Cphi_rgb_int); set(gca,'YDir','normal');
end
end
if fig4_suppl
% % Plot raw BASKET data for sens analysis, merged
font_scaling = 1.0;
linewidth=linewidth_def;
markersize=markersize_def;
FS_axislabels=FS_axislabels_def*font_scaling;
FS_axis=FS_axis_def*font_scaling;
cell2plot=1;
% Convert our firing rate cell arrays into matricies, extracting
% out a specific cell number
[pm_zeit_single1 pm_single1 pm_ste_single1] = extract_cell_zeit(cell2plot,pm_zeit_cell1, pm_cell1, pm_ste_cell1);
[pm_zeit_single2 pm_single2 pm_ste_single2] = extract_cell_zeit(cell2plot,pm_zeit_cell2, pm_cell2, pm_ste_cell2);
bC_phi=[bC_phi1 bC_phi2];
bC_err=[bC_err1 bC_err2];
pmzs_merg=[pm_zeit_single1 pm_zeit_single2];
pms_merg=[pm_single1 pm_single2];
pmss_merg=[pm_ste_single1 pm_ste_single2];
plot_error=0;
figure1 = figure;
set (figure1, 'Position',[524 339 560*3/2 420]*font_scaling,'Color','w');
subplot(121);
ind = find((bC_phi > 6) & (~bC_err));
if plot_error; errorbar(pmzs_merg(:,ind),pms_merg(:,ind),pmss_merg(:,ind)); else
plot(pmzs_merg(:,ind),pms_merg(:,ind),'--'); end
xlabel('Time (hours)', 'FontSize',FS_axislabels);
ylabel('firing rate (s^{-1})', 'FontSize',FS_axislabels);
title('B firing rate noon, merged', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 ylimits(2)]);
xlim= get(gca,'XLim');
xtickarr = xlim(1):6:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
subplot(122);
ind = find((bC_phi < 6) & (~bC_err));
if plot_error; errorbar(pmzs_merg(:,ind),pms_merg(:,ind),pmss_merg(:,ind)); else
plot(pmzs_merg(:,ind),pms_merg(:,ind),'--'); end
xlabel('Time (hours)', 'FontSize',FS_axislabels);
title('B firing rate midnight, merged', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 ylimits(2)]);
xlim= get(gca,'XLim');
xtickarr = xlim(1):6:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
% % Plot raw BASKET data for sens analysis, not merged
cell2plot=1;
[pm_zeit_single1 pm_single1 pm_ste_single1] = extract_cell_zeit(cell2plot,pm_zeit_cell1, pm_cell1, pm_ste_cell1);
[pm_zeit_single2 pm_single2 pm_ste_single2] = extract_cell_zeit(cell2plot,pm_zeit_cell2, pm_cell2, pm_ste_cell2);
bC_phi=[bC_phi1 ];
bC_err=[bC_err1 ];
pmzs_merg=[pm_zeit_single1 ];
pms_merg=[pm_single1 ];
pmss_merg=[pm_ste_single1 ];
font_scaling = 0.5;
linewidth=linewidth_def;
markersize=markersize_def;
FS_axislabels=FS_axislabels_def*font_scaling;
FS_axis=FS_axis_def*font_scaling;
figure1 = figure;
set (figure1, 'Position',[524 339 560*3/2 420*7/4]*font_scaling,'Color','w');
subplot(221);
ind = find((bC_phi > 6) & (~bC_err));
if plot_error; errorbar(pmzs_merg(:,ind),pms_merg(:,ind),pmss_merg(:,ind)); else
plot(pmzs_merg(:,ind),pms_merg(:,ind),'--'); end
xlabel('Time (hours)', 'FontSize',FS_axislabels);
ylabel('firing rate (s^{-1})', 'FontSize',FS_axislabels);
title('Bas FR phase noon, msg2b', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 ylimits(2)]);
xlim= get(gca,'XLim');
xtickarr = xlim(1):6:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
subplot(222);
ind = find((bC_phi < 6) & (~bC_err));
if plot_error; errorbar(pmzs_merg(:,ind),pms_merg(:,ind),pmss_merg(:,ind)); else
plot(pmzs_merg(:,ind),pms_merg(:,ind),'--'); end
xlabel('Time (hours)', 'FontSize',FS_axislabels);
title('Bas FR phase midnight, msg2b', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 ylimits(2)]);
xlim= get(gca,'XLim');
xtickarr = xlim(1):6:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
bC_phi=[bC_phi2 ];
bC_err=[bC_err2 ];
pmzs_merg=[pm_zeit_single2 ];
pms_merg=[pm_single2 ];
pmss_merg=[pm_ste_single2 ];
subplot(223);
ind = find((bC_phi > 6) & (~bC_err));
if plot_error; errorbar(pmzs_merg(:,ind),pms_merg(:,ind),pmss_merg(:,ind)); else
plot(pmzs_merg(:,ind),pms_merg(:,ind),'--'); end
xlabel('Time (hours)', 'FontSize',FS_axislabels);
ylabel('firing rate (s^{-1})', 'FontSize',FS_axislabels);
title('Bas FR noon, chop', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 ylimits(2)]);
xlim= get(gca,'XLim');
xtickarr = xlim(1):6:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
subplot(224);
ind = find((bC_phi < 6) & (~bC_err));
if plot_error; errorbar(pmzs_merg(:,ind),pms_merg(:,ind),pmss_merg(:,ind)); else
plot(pmzs_merg(:,ind),pms_merg(:,ind),'--'); end
xlabel('Time (hours)', 'FontSize',FS_axislabels);
title('Bas FR phase midnight, chop', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 ylimits(2)]);
xlim= get(gca,'XLim');
xtickarr = xlim(1):6:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
% % Plot raw BASKET data for just chop data
cell2plot=1;
[pm_zeit_single2 pm_single2 pm_ste_single2] = extract_cell_zeit(cell2plot,pm_zeit_cell2, pm_cell2, pm_ste_cell2);
font_scaling = 0.5;
linewidth=linewidth_def;
markersize=markersize_def;
FS_axislabels=FS_axislabels_def*font_scaling;
FS_axis=FS_axis_def*font_scaling;
figure1 = figure;
set (figure1, 'Position',[524 339 560*3/2 420*7/4]*font_scaling,'Color','w');
bC_phi=[bC_phi2 ];
bC_err=[bC_err2 ];
pmzs_merg=[pm_zeit_single2 ];
pms_merg=[pm_single2 ];
pmss_merg=[pm_ste_single2 ];
subplot(221);
ind = find((bC_phi > 6) & (~bC_err));
if plot_error; errorbar(pmzs_merg(:,ind),pms_merg(:,ind),pmss_merg(:,ind)); else
plot(pmzs_merg(:,ind),pms_merg(:,ind)); end
xlabel('Time (h)', 'FontSize',FS_axislabels);
ylabel('Firing rate (s^{-1})', 'FontSize',FS_axislabels);
% title('Bas FR noon, chop', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 ylimits(2)]);
xlim= get(gca,'XLim');
xtickarr = xlim(1):6:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
subplot(222);
ind = find((bC_phi < 6) & (~bC_err));
if plot_error; errorbar(pmzs_merg(:,ind),pms_merg(:,ind),pmss_merg(:,ind)); else
plot(pmzs_merg(:,ind),pms_merg(:,ind)); end
xlabel('Time (h)', 'FontSize',FS_axislabels);
ylabel('Firing rate (s^{-1})', 'FontSize',FS_axislabels);
% title('Bas FR phase midnight, chop', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 ylimits(2)]);
xlim= get(gca,'XLim');
xtickarr = xlim(1):6:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
subplot(223);
ind = find(bC_err);
if plot_error; errorbar(pmzs_merg(:,ind),pms_merg(:,ind),pmss_merg(:,ind)); else
plot(pmzs_merg(:,ind),pms_merg(:,ind)); end
xlabel('Time (h)', 'FontSize',FS_axislabels);
% title('Bas FR phase midnight, chop', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 ylimits(2)]);
xlim= get(gca,'XLim');
xtickarr = xlim(1):6:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
ylabel('Firing rate (s^{-1})', 'FontSize',FS_axislabels);
% % Plot raw PYR data for sens analysis, merged
cell2plot=4;
% Convert our firing rate cell arrays into matricies, extracting
% out a specific cell number
[pm_zeit_single1 pm_single1 pm_ste_single1] = extract_cell_zeit(cell2plot,pm_zeit_cell1, pm_cell1, pm_ste_cell1);
[pm_zeit_single2 pm_single2 pm_ste_single2] = extract_cell_zeit(cell2plot,pm_zeit_cell2, pm_cell2, pm_ste_cell2);
% bC_phi=[bC_phi1 bC_phi2];
% bC_err=[bC_err1 bC_err2];
% pmzs_merg=[pm_zeit_single1 pm_zeit_single2];
% pms_merg=[pm_single1 pm_single2];
% pmss_merg=[pm_ste_single1 pm_ste_single2];
bC_phi=[bC_phi2];
bC_err=[bC_err2];
pmzs_merg=[pm_zeit_single2];
pms_merg=[pm_single2];
pmss_merg=[pm_ste_single2];
% figure1 = figure;
% set (figure1, 'Position',[524 339 560 420]*font_scaling,'Color','w');
subplot(224)
ind = find((~bC_err) | (bC_err));
if plot_error; errorbar(pmzs_merg(:,ind),pms_merg(:,ind),pmss_merg(:,ind)); else
plot(pmzs_merg(:,ind),pms_merg(:,ind)); end
xlabel('Time (h)', 'FontSize',FS_axislabels);
ylabel('Firing rate (s^{-1})', 'FontSize',FS_axislabels);
% title('Pyr firing rate', 'FontSize',FS_axislabels);
ylimits = get(gca,'YLim'); xlimits = get(gca,'XLim');
axis([-2 24 ylimits(1)-1 ylimits(2)]);
xlim= get(gca,'XLim');
xtickarr = xlim(1):6:xlim(2);
set(gca,'XTick',xtickarr,'XTickLabel',xtickarr);
% annotation(figure1,'textbox',[0.088 0.97 0.02464 0.0619],'String',{'a'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
% annotation(figure1,'textbox',[0.37 0.97 0.02464 0.0619],'String',{'b'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
% annotation(figure1,'textbox',[0.66 0.97 0.02464 0.0619],'String',{'c'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
annotation(figure1,'textbox',[0.03 0.92 0.05455 0.08571],'String',{'A'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
annotation(figure1,'textbox',[0.48 0.92 0.05455 0.08571],'String',{'B'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
annotation(figure1,'textbox',[0.03 0.45 0.05455 0.08571],'String',{'C'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
annotation(figure1,'textbox',[0.48 0.45 0.05455 0.08571],'String',{'D'},'FitBoxToText','off','LineStyle','none','FontSize',FS_axislabels*2);
end
clear set_values set_values_multi