%plotVNai.m
%Jessica Parker, October 10, 2024
%
%This matlab script is used to produce a simple plot of the voltage and [Na+]i over time.
clear all;
close all;
mrk = 'sc';
run1 = 2;
run2 = 0;
run3 = 0;
run4i = 2;
run4f = 2;
run5i = 1;
run5f = 89;
skpRun5 = 10; % Set number of run5 instances to skip in between plotting, skips [skpRun5-1] traces in between plotting
run6i = 1;
run6f = 1;
datadir = 'data/';
prfx = 'V';
nvar = 1;
vsblty = 'on';
CloseFigs = 1;
DisplayActivityType = 0; % Set to 1 to include text in the figure that says whether it is silent, spiking, or bursting
DisplayBurstChars = 1; % Set to 1 to display burst period (BP), burst duration (BD), and interburst interval (IBI) at the top
figMrk = '';
xmin0 = 0; %Set the time range that you want to plot
xmax0 = 1;
%% ShowParameterAsTitle and OtherTitle cannot both be 1, but they can both be 0
ShowParameterAsTitle = 1; %boolean, set to 1 if you want a parameter value in the title
parname = '[Na^+]_i'; %Name of parameter to show in the title
parunits = 'mM'; %Units of parameter to show in the title
parcan = 35; %set to initial parameter value in sweep
parstep = -0.25; %set to parameter step size in sweep
titlExtra = ''; %% Anything extra that you want to put at the end of the title. Set to '' if you don't want to add anything.
Sweeping2Pars = 0; %% Use this by setting it to 1 if ShowParameterAsTitle is set to 1 and there are 2 parameters being varied.
SweepingIndependently = 0; %% Set SweepingIndependently to 1 if the two parameters are swept independently and referenced by different run numbers.
parname2 = 'I_{PumpMax}'; %% If SweepingIndependently is set to 1, the first parameter that you set as "parname" should
parunits2 = 'pA'; %% be the one represented by run4 and the second that you set as "parname2" should be the one represented by run5.
parcan2 = 50;
parstep2 = 0.5;
OtherTitle = 0; %% Use this if you want to have something else as the title where all plots will have the same title.
titlText = ''; %% Text you want to put in the title of all plots
nFigRows = 1;
titles = {'V_m (mV)'};
tint = 0.0001; %Time step between data points
fntsz = 14; %Font size
fntnm = 'Lucida Sans';
dir2 = [num2str(run1) '_' num2str(run2) '_' num2str(run3)];
aa = 1;
for run4=run4i:run4f
typesFound = 0;
if DisplayActivityType && exist([datadir 'type' dir2 '_' num2str(run4) mrk '.txt'])
typ = load([datadir 'type' dir2 '_' num2str(run4) mrk '.txt']);
typesFound = 1;
types = {'Bursting','Spiking','Silence','Depolarization Block','Depolarized Oscillations','Unknown','Plateau Bursting'};
mrk3 = 'Bd';
else
mrk3 = '';
end
for run5=run5i:skpRun5:run5f
yy = [];
for run6=run6i:run6f %Concatenating portions of time saved in separate files
dir3 = [dir2 '_' num2str(run4) '_' num2str(run5)];
VarN=[datadir prfx dir3 '_' num2str(run6) '.dat'];
f1=fopen(VarN);
yy1=fread(f1,[nvar, 10000000],'double')';
fclose(f1);
yy = [yy; yy1(1:end-1,:)]; %Remove last point here, because otherwise
end %you will repeat the same time point
%twice between consecutive run6 files
lnt = length(yy(:,1));
tt = 0:tint:tint*(lnt-1);
plotDat = zeros(length(yy(:,1)),2);
plotDat(:,1) = yy(:,1)';
xmin = xmin0;
xmax = xmax0;
BurstingFound = 0;
if DisplayBurstChars
if exist([datadir 'bd1j' dir3 '_' num2str(run6f) mrk '.txt'])
bc = load([datadir 'bd1j' dir3 '_' num2str(run6f) mrk '.txt']);
BurstingFound = 1;
elseif exist([datadir 'plts' dir3 '_' num2str(run6f) mrk '.txt'])
bc = load([datadir 'plts' dir3 '_' num2str(run6f) mrk '.txt']);
BurstingFound = 1;
end
end
pgBttm = 0.75;
if DisplayActivityType || DisplayBurstChars
pgTop = 0.75;
else
pgTop = 0.5;
end
figSep = 0.2;
figHght = 1.25;
pgHght = nFigRows*figHght + pgBttm + pgTop + (nFigRows-1)*figSep;
f = figure('visible',vsblty);
f.PaperPositionMode = 'manual';
f.PaperUnits = 'inches';
f.Units = 'inches';
f.OuterPosition = [1.0 1.0 8.5 pgHght+1.0];
f.InnerPosition = [0.25 0.25 8 pgHght+0.5];
f.PaperPosition = [0.25 0.25 7.5 pgHght];
f.RendererMode = 'manual';
figHght0 = (pgHght-pgBttm-pgTop-(nFigRows-1)*figSep)/nFigRows;
topPerc = 1 - pgTop/pgHght;
bttmPerc = pgBttm/pgHght;
restPerc = topPerc - bttmPerc;
sepPerc = figSep/pgHght;
if DisplayActivityType && typesFound
axes('position',[0.7 topPerc 0.3 1-topPerc]);
text(0,0.75,types{typ(run5-run5i+1)},'fontname',fntnm,'fontsize',fntsz-3);
axis([0 1 0 1]);
axis off;
elseif DisplayActivityType && ~typesFound
disp(['Could not find activity types file for run4 = ' num2str(run4)]);
end
if DisplayBurstChars && BurstingFound
axes('position',[0.2 topPerc 0.7 1-topPerc]);
bcText = ['BP = ' num2str(round(mean(bc(2,:)),2)) ' s, BD = ' num2str(round(mean(bc(3,:)),3)) ' s, IBI = ' num2str(round(mean(bc(4,:)),2)) ' s'];
text(0,0.6,bcText,'fontname',fntnm,'fontsize',fntsz);
axis([0 1 0 1]);
axis off;
end
for bb = 1:nFigRows
axes('position',[0.15 topPerc-(restPerc/nFigRows)*bb 0.8 restPerc/nFigRows-sepPerc]);
plot(tt,plotDat(:,bb),'k-','linewidth',1.5);
hold on;
xlim([xmin xmax]);
if max(plotDat(:,bb)) - min(plotDat(:,bb)) > 0.01*abs(mean(plotDat(:,bb)))
ymin = min(plotDat(:,bb));
ymax = max(plotDat(:,bb));
yl = ymax - ymin;
ylim([ymin-0.1*yl ymax+0.1*yl]);
if bb == 2
ylim([ymin-0.2*yl ymax+0.2*yl]);
end
else
ymin = mean(plotDat(:,bb))-0.05*abs(mean(plotDat(:,bb)));
ymax = mean(plotDat(:,bb))+0.05*abs(mean(plotDat(:,bb)));
ylim([ymin ymax]);
end
ylabel(titles{bb});
if bb == 1
if ShowParameterAsTitle
if Sweeping2Pars && ~SweepingIndependently
title([parname ' = ' num2str(parcan+parstep*(run5-1)) ' ' parunits ', ' parname2 ' = ' num2str(parcan2+parstep2*(run5-1)) ' ' parunits2 titlExtra]);
elseif Sweeping2Pars
title([parname ' = ' num2str(parcan+parstep*(run4-1)) ' ' parunits ', ' parname2 ' = ' num2str(parcan2+parstep2*(run5-1)) ' ' parunits2 titlExtra]);
else
title([parname ' = ' num2str(parcan+parstep*(run5-1)) ' ' parunits titlExtra]);
end
elseif OtherTitle
title(titlText);
end
end
if bb == nFigRows
xlabel('Time (s)');
else
xticks([]);
end
box off;
ax = gca;
ax.FontName = fntnm;
ax.FontSize = fntsz;
ax.LineWidth = 2.0;
end
print(f,['plots/V' dir3 '_' num2str(run6) mrk3 figMrk '.eps'],'-depsc','-r0');
if strcmp(vsblty,'off')
close(f);
elseif CloseFigs
close(f);
end
aa = aa + 1;
end
end