Hyperexcitable-GC-MATLAB/plot_fig8.m at main · selenasingh/Hyperexcitable-GC-MATLAB · GitHub

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%%%% plot aradi and holmes fig 8 %%%%%
%%% reducing skdr conductance increases bursting %%%

%NORMAL
initparams
t_startinj = 0;
t_stopinj = 200;
t_run = 300;

I_ext = 90;
[g,e,elecparam, calciump] = setparams(gna, gfkdr, gskdr, gka, gtca, gnca, glca, gbk, gsk, ggaba, gkir, gleak, ena, ek, ecl, ekir, C, I_ext, tau, reCa, B, depth, F, t_startinj, t_stopinj);
declareglobal(g, e, elecparam, calciump);
tspan = [0; t_run];
y0 = [V_m; m_0; h_0; nf_0; ns_0; k_0; l_0; a_0; b_0; c_0; d_0; e_0; tcai_0; ncai_0; lcai_0; r_0; s_0; q_0; p_0];
[t,y] = ode15s(@granulecell, tspan, y0);

fig = figure();
tiledlayout(2,1)
nexttile
plot(t, y(:,1))
xlabel('Time (ms)')
ylabel ('Voltage (mV')


%%% reduce skdr by 90%

initparams
gskdr = gskdr * 0.1;

t_startinj = 0;
t_stopinj = 200;
t_run = 300;

I_ext = 90;
[g,e,elecparam, calciump] = setparams(gna, gfkdr, gskdr, gka, gtca, gnca, glca, gbk, gsk, ggaba, gkir, gleak, ena, ek, ecl, ekir, C, I_ext, tau, reCa, B, depth, F, t_startinj, t_stopinj);
declareglobal(g, e, elecparam, calciump);
tspan = [0; t_run];
y0 = [V_m; m_0; h_0; nf_0; ns_0; k_0; l_0; a_0; b_0; c_0; d_0; e_0; tcai_0; ncai_0; lcai_0; r_0; s_0; q_0; p_0];
[t,y] = ode15s(@granulecell, tspan, y0);

nexttile
txt = 'g_{skdr} reduced by 90%';
plot(t, y(:,1), 'DisplayName', txt)
legend('location', 'best')
xlabel('Time (ms)')
ylabel ('Voltage (mV')

%%%%%%%%%%%%%%%%% IF curves %%%%%%%%%%%%%%%%%%%
initparams
i_ext = 30:1:200 ;

t_startinj = 100;
t_stopinj = 500;
t_run = 550;

clear freq i_store
for i=1:length(i_ext)
    I_ext = i_ext(i);
    [g,e,elecparam, calciump] = setparams(gna, gfkdr, gskdr, gka, gtca, gnca, glca, gbk, gsk, ggaba, gkir, gleak, ena, ek, ecl, ekir, C, I_ext, tau, reCa, B, depth, F, t_startinj, t_stopinj);
    declareglobal(g, e, elecparam, calciump);
    tspan = [0; t_run];
    y0 = [V_m; m_0; h_0; nf_0; ns_0; k_0; l_0; a_0; b_0; c_0; d_0; e_0; tcai_0; ncai_0; lcai_0; r_0; s_0; q_0; p_0];
    [t,y] = ode15s(@granulecell, tspan, y0);% options);
    if max(t) == t_run
        freq(i) = length(findpeaks(y(:,1), 'MinPeakHeight', -10));
        i_store(i) = i_ext(i);
    end
    comb = [i_store; freq];
    comb( :, all(~comb,1) ) = []; %remove 0s.

end

fig2 = figure();
hold on
plot(comb(1,:), comb(2,:), '-o')


gskdr = gskdr * 0.1;
clear freq i_store
for i=1:length(i_ext)
    I_ext = i_ext(i);
    [g,e,elecparam, calciump] = setparams(gna, gfkdr, gskdr, gka, gtca, gnca, glca, gbk, gsk, ggaba, gkir, gleak, ena, ek, ecl, ekir, C, I_ext, tau, reCa, B, depth, F, t_startinj, t_stopinj);
    declareglobal(g, e, elecparam, calciump);
    tspan = [0; t_run];
    y0 = [V_m; m_0; h_0; nf_0; ns_0; k_0; l_0; a_0; b_0; c_0; d_0; e_0; tcai_0; ncai_0; lcai_0; r_0; s_0; q_0; p_0];
    [t,y] = ode15s(@granulecell, tspan, y0);% options);
    if max(t) == t_run
        freq(i) = length(findpeaks(y(:,1), 'MinPeakHeight', -10));
        i_store(i) = i_ext(i);
    end
    comb = [i_store; freq];
    comb( :, all(~comb,1) ) = []; %remove 0s.

end
plot(comb(1,:), comb(2,:), '-o')

hold off

legend({'Control', 'g_{skdr} reduced by 90%'})
xlabel('I_{ext} (pA)')
ylabel('Number of Spikes')

saveas(fig, 'plot_redgskdr.jpeg')
saveas(fig2, 'plot_redgskdr_IF.jpeg')