clear all; clc;
%%
Helix_up= 1;
Helix_down = 0;
grid = 0;
place = 1;
%%
if Helix_up
traj_file='Trajectory_fivecoil_up.csv';
spike_file='encoded_helix_t20p1_b1.5pi_3d_test_up.csv';
else
traj_file='Trajectory_fivecoil_down.csv';
spike_file='encoded_helix_t20p1_b1.5pi_3d_test_down.csv';
end
traj_data=csvread(traj_file);
spike_data=csvread(spike_file);
%%
if grid
g_cells = [2,3,29,35,39,40,42,44,47];
cells = g_cells;
else
p_cells = [1, 6, 8, 15, 18, 19, 20, 21, 23, 24, 27, 31, 34, 36, 41, 43, 45, 46, 48];
cells = p_cells;
end
%% seperate all the coils
num_coils = 5; coil_dat = {}; coil_dat_spk = {};
edge_hist = 1:6:360;
for k = cells
angles = [];
ot = spike_data(:,k);
ot_mean = mean(ot);
ot_std = std(ot);
thresh = ot_mean + 1.5*ot_std;
spk_cell = ot > thresh;
dat = [traj_data spk_cell];
for i = 1:num_coils
if i == num_coils
temp = i>=traj_data(:,3) & traj_data(:,3)>=(i-1) ;
else
temp = i>traj_data(:,3) & traj_data(:,3)>=(i-1);
end
temp_coil = dat(temp,:); temp_coil_spk = temp_coil(temp_coil(:,4)==1, :);
coil_dat{k,i} = temp_coil;
coil_dat_spk{k,i} = temp_coil_spk;
ang = quad(temp_coil(:,1), temp_coil(:,2));
angles = [angles ang.*temp_coil(:,4)];
end
figure()
for p = 1:num_coils
subplot(5,1,num_coils-p+1)
histogram(angles(angles(:, p) > 0, p), edge_hist, 'FaceColor','#ff4d01','EdgeColor','#ff4d01')
xlim([0 360]);
% axis on;
set(gca,'XTick',[]); set(gca,'YTick',[])
axis on;
end
sgtitle(['neuron ', num2str(k)]);
% break;
savefig(['place_3D_lin', num2str(k)]);
saveas(gcf, ['place_3D_lin', num2str(k), '.png'])
end
% %% plotting histogram
% p = k; figure()
% firr = spike_data(:,p) > (0.4*max(spike_data(:,p)));
% scatter3(traj_data(:,1), traj_data(:,2), traj_data(:,3)); hold on
% scatter3(traj_data(firr,1), traj_data(firr,2), traj_data(firr,3), 'MarkerFaceColor', 'red', 'MarkerEdgeColor','red')
% hold off;
%% ############## All Statistical Analysis and Plots for the manuscript for Helix ###################
%% t-test2 minor axis flat arena and helical maze (Place cells)
place_2d_minor = [0.1760485701 0.3229981902 0.5495352998 0.5235088226 0.4103321728 0.2618040259 0.6348144702 0.3818947259 0.2426696942 0.4856625345 0.04618802154 0.3337530245 0.3975651699 0.2342174095 0.07096424943 0.167710531 0.5396179497 0.07779652996 0.07302967433 0.08326663998 0.4420635688 0.04618802154 0.1292714629 0.6348500116 0.3967947356 0.430313642 0.1596428675 0.3864839154 0.07344809129 0.4223801212 0.1110899828 0.6087874189 0.1593915278 0.2190659415 0.3075356453];
place_3d_minor = [0.84524 0.553228 0.581896 0.43616 0.704888 0.355072 0.51438 0.546812 0.48892 0.536308 0.257164 1.12132 0.154164 0.046188 0.337916 0.402792 0.349768 0.650408 0.787632 0.336856 0.472176 0.531224 0.444852 0.522744 0.47112 0.55718 0.482044 0.21294 0.3989 0.10328 0.34954 0.34372 0.510324 0.244212 0.569104 0.236196 0.236196 0.939092 0.598516 0.552532 0.409744 0.386288 0.594652 0.477864 0.52892 0.281416 0.551468 0.468632 0.524804 0.21802 0.21802 0.166532 1.179956 0.625804 0.324912 0.4026 0.380872 0.650772 0.768444 0.293868 0.461972 0.497328 0.453156 0.539472 0.409576 0.549128 0.495784 0.391908 0.391372 0.3325 0.344332 0.544868 0.242712 0.5837 0.245676 0.245676];
[h, p, ci, stats] = ttest2(place_2d_minor, place_3d_minor);
place_2d_minor_mean = mean(place_2d_minor);
place_2d_minor_std = std(place_2d_minor);
place_3d_minor_mean = mean(place_3d_minor);
place_3d_minor_std = std(place_3d_minor);
%% ttest2 minor axis Helical and major axis flat arena (Place cells)
% place_3d_minor = [0.785, 1.256, 0.942, 0.471, 0.471, 0.471, 1.256, 0.628, 1.256, 0.471, 0.471, 0.471, 0.785, 0.785, 0.942, 1.413, 0.785, 0.785, 0.785, 0.785, 1.256, 0.628, 0.471, 1.57, 0.785, 0.785, 0.785, 0.628, 0.942, 0.785, 0.942, 1.099, 0.942, 0.785, 0.628, 0.942, 0.942, 0.471, 0.942, 0.785, 2.983, 0.628, 0.785, 0.628, 0.471, 1.256, 1.413, 0.628, 0.942, 0.628, 0.785, 0.942, 0.628, 1.256, 1.256, 0.942, 0.942, 0.628, 0.785, 0.628, 0.471, 0.942, 0.785, 0.942, 0.942, 0.942, 0.942, 2.041, 0.628, 0.628, 0.785, 0.628, 0.471, 0.785, 1.099, 1.256, 0.785, 0.942, 1.099, 0.628, 1.57, 0.628, 0.628, 0.628, 0.628, 1.099, 0.628, 0.628, 0.471, 2.198, 0.942, 1.256, 0.942, 0.785, 1.099, 0.628, 0.628, 0.628, 1.099, 0.942, 0.628, 0.785, 0.628, 0.785, 0.942, 1.099, 0.785, 0.471, 0.471, 1.099, 0.785, 0.785, 0.628, 0.471, 0.785, 0.471, 0.471, 1.256, 0.942, 1.256, 0.628, 0.942, 0.785, 0.785, 0.471, 0.785, 1.256, 1.099, 0.628, 0.471, 1.413, 0.471, 0.942, 1.413, 0.942, 0.785, 1.099, 1.099, 1.099, 0.785, 0.471, 0.628, 0.785, 1.099, 0.471, 0.942, 1.256, 0.628, 0.628, 0.628, 0.628, 0.785, 1.57, 0.785, 0.628, 0.628, 1.413, 0.942, 0.942, 0.942, 0.628, 1.099, 1.256, 0.628, 0.628, 1.413, 0.942, 0.942, 0.628, 0.628, 0.942, 0.785, 0.628, 0.628, 0.785, 0.785, 0.628, 0.942, 1.256, 0.785, 1.256, 0.942, 0.785, 0.785, 1.256, 0.628, 0.628, 0.628, 1.57, 0.942, 0.942, 0.785, 0.628, 1.256, 0.471, 0.785, 1.57, 0.785, 1.57, 1.413, 0.942, 0.785, 0.471, 1.099, 0.628, 1.099, 0.785, 0.942, 0.785, 0.471, 0.785, 0.942, 0.785, 0.942, 1.256, 0.628, 0.628, 0.785];
% place_2d_major = [0.777752852121663, 0.758594785132971, 0.537943452755943, 0.667326390651934, 0.395897327444314, 0.681362986691869, 0.596664984468103, 0.478108448723749, 0.490488303119163, 0.62276701592062, 0.476129430444291, 0.392740974102209, 0.605318697475111, 0.670807008654466, 0.614283245504354, 0.387160302842611, 0.481696289501409, 0.452687345379351, 0.602818139911889, 0.459052066694343, 0.58526177303878, 0.529233170547014, 0.600765033338677, 0.490172632278071, 0.641731324666737, 0.424264358794166, 0.637397996304046, 0.675702336766034, 0.619047379915457, 0.591873426115854, 0.536152821412371, 0.490746185643246, 0.482261739103446, 0.519923200327112, 0.680178804999432, 0.66676174197458, 0.329914439536929, 0.629760713012783, 0.588873690334626, 0.433790180777203, 0.655141529593263, 0.357794688279649, 0.425997808795614, 0.362905883490623, 0.731076630544209, 0.659572877473163, 0.362905883490623, 0.401358238203914, 0.52017765041616, 0.634959972118166, 0.45560794343492, 0.422738662826946, 0.735250100520483, 0.762344622243946];
% [h, p, ci, stats] = ttest2(place_3d_minor, place_2d_major);
% place_3d_minor_mean = mean(place_3d_minor);
% place_3d_minor_std = std(place_3d_minor);
% place_2d_major_mean = mean(place_2d_major);
% place_2d_major_std = std(place_2d_major);
%% ttest2 major and minor axis helical (Place cells)
place_3d_minor = [0.84524 0.553228 0.581896 0.43616 0.704888 0.355072 0.51438 0.546812 0.48892 0.536308 0.257164 1.12132 0.154164 0.046188 0.337916 0.402792 0.349768 0.650408 0.787632 0.336856 0.472176 0.531224 0.444852 0.522744 0.47112 0.55718 0.482044 0.21294 0.3989 0.10328 0.34954 0.34372 0.510324 0.244212 0.569104 0.236196 0.236196 0.939092 0.598516 0.552532 0.409744 0.386288 0.594652 0.477864 0.52892 0.281416 0.551468 0.468632 0.524804 0.21802 0.21802 0.166532 1.179956 0.625804 0.324912 0.4026 0.380872 0.650772 0.768444 0.293868 0.461972 0.497328 0.453156 0.539472 0.409576 0.549128 0.495784 0.391908 0.391372 0.3325 0.344332 0.544868 0.242712 0.5837 0.245676 0.245676];
place_3d_major = [5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 1 5 5 5 3 5 5 5 2 2 1 5 3 5 1 5 1 1 5 5 5 5 4 5 5 5 1 5 5 5 2 1 5 5 5 5 5 5 5 5 1 5 5 5 5 5 5 5 5 4 5 5 5 4 5 1 1];
[h, p, ci, stats] = ttest2(place_3d_minor, place_3d_major);
place_3d_minor_mean = mean(place_3d_minor);
place_3d_minor_std = std(place_3d_minor);
place_3d_major_mean = mean(place_3d_major);
place_3d_major_std = std(place_3d_major);
% plot(1:230, place_3d_major)
%% ttest2 aspect ratio aspect ratio helical and 2d (place cells)
place_3d_aspectR = [5.915479627 9.037865039 8.59260074 11.46368305 7.093325464 14.08165105 9.720440142 9.143910521 10.22662194 9.323000962 19.44284581 4.459030428 32.43299344 108.2532259 14.79657666 12.41335478 14.29518995 7.687482319 6.34814228 2.968627544 10.5892718 9.412225351 11.2396932 5.738946788 10.6130073 8.973760724 10.37249712 9.392317085 5.013787917 9.682416731 14.3045145 8.728034447 9.797697149 4.094802876 8.785740392 4.233771952 4.233771952 5.324291976 8.353995549 9.049249636 12.20274122 12.94371039 6.726623302 10.46322803 9.453225441 17.76729113 1.813341844 10.6693525 9.527366407 22.93367581 9.173470324 6.00485192 4.237446142 7.989722022 15.38878219 12.41927471 13.12776996 7.683182436 6.506655007 17.01444186 2.164633354 10.05372712 11.0337279 9.268321618 12.20774655 9.105345202 10.08503703 12.75809629 12.77556902 12.03007519 14.52086939 9.1765345 20.60054715 6.852835361 20.35200834 4.070401667];
place_2d_aspectR = [2.904928466 2.475974833 1.415131231 1.527976687 1.439957401 1.127139174 1.092725463 1.416433403 2.058418221 1.154840966 2 1.923112226 1.421609739 1.283074299 2.809996831 2.426163615 1.441112266 3.933868321 2 1.467598771 1.262814562 4 1.82185316 1.108666796 1.78749679 1.272893473 3.071448571 1.359898364 3.003033072 1.492775262 3.119286799 1.142316185 2.525470603 2.576393719 1.843020881];
[h, p, ci, stats] = ttest2(place_3d_aspectR, place_2d_aspectR);
place_3d_aspectR_mean = mean(place_3d_aspectR);
place_3d_aspectR_std = std(place_3d_aspectR);
place_2d_aspectR_mean = mean(place_2d_aspectR);
place_2d_aspectR_std = std(place_2d_aspectR);
%% field extend in coils (PLAce cells)
place_3d_major = [5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 1 5 5 5 3 5 5 5 2 2 1 5 3 5 1 5 1 1 5 5 5 5 4 5 5 5 1 5 5 5 2 1 5 5 5 5 5 5 5 5 1 5 5 5 5 5 5 5 5 4 5 5 5 4 5 1 1];
%place_3d_major = [4, 1, 1, 1, 3, 2, 5, 5, 3, 2, 1, 1, 5, 3, 2, 3, 2, 1, 1, 1, 4, 3, 3, 2, 1, 5, 4, 3, 2, 2, 5, 5, 3, 2, 2, 3, 2, 5, 2, 5, 5, 4, 1, 1, 1, 3, 3, 2, 2, 1, 5, 3, 3, 2, 5, 5, 2, 2, 1, 1, 1, 4, 4, 2, 2, 1, 1, 4, 3, 4, 2, 2, 2, 1, 5, 2, 2, 1, 5, 2, 3, 2, 1, 1, 1, 5, 3, 3, 1, 5, 4, 1, 1, 3, 2, 2, 2, 1, 3, 3, 2, 1, 1, 4, 5, 3, 2, 1, 1, 5, 5, 2, 4, 1, 1, 1, 3, 2, 5, 5, 3, 2, 1, 1, 5, 3, 2, 3, 2, 1, 1, 1, 4, 3, 3, 2, 1, 5, 4, 3, 2, 2, 5, 5, 3, 2, 2, 3, 2, 5, 2, 5, 5, 4, 1, 1, 1, 3, 3, 2, 2, 1, 5, 3, 3, 2, 5, 5, 2, 2, 1, 1, 1, 4, 4, 2, 2, 1, 1, 4, 3, 4, 2, 2, 2, 1, 5, 2, 2, 1, 5, 2, 3, 2, 1, 1, 1, 5, 3, 3, 1, 5, 4, 1, 1, 3, 2, 2, 2, 1, 3, 3, 2, 1, 1, 4, 5, 3, 2, 1, 1, 5, 5, 2];
count5 = sum(place_3d_major == 5);
count4 = sum(place_3d_major == 4);
count3 = sum(place_3d_major == 3);
count2 = sum(place_3d_major == 2);
count1 = sum(place_3d_major == 1);
X = [1,2,3,4,5];
sum_count = count1 + count2 + count3 + count4 + count5;
Y = [count1*100/(sum_count), count2*100/(sum_count), count3*100/(sum_count), count4*100/(sum_count), count5*100/(sum_count)];
figure;
bar(X, Y, 'FaceColor','#808080');
xlabel("Vertical field size (coils)");
ylabel("Percentage fields");
set(gca, 'FontSize', 20);
%% t-test2 minor axis flat arena and helical maze (Grid cells)
grid_2d_minor = [0.6207601075 0.1886146333 0.4178419166 0.2070223147 0.4150641774 0.1535395488 0.1360547741 0.4199236926 0.5834560761 0.3064781682 0.1688573083 0.4854188646 0.4990691328 0.1337216794 0.2331584889 0.1062078215 0.3149181194 0.3908220658 0.2277678779 0.2219151459 0.3051874927 0.4063136432 0.2871462467 0.2377255883 0.2307782242 0.1154700538 0.1154700538 0.1680581342 0.05773502692];
grid_3d_minor = [0.46474 0.551735 0.344095 0.754665 0.517965 0.517155 0.591845 0.4119 0.54633 0.23805 0.76189 0.39096 0.87562 0.452965 0.738285 0.48321 0.462525 0.33785 0.4483907304 0.5714453888 0.8580920657 0.5053760316 0.4947534898 0.3591251 0.438195039 0.6236926937 0.3902599898 0.5803358673 0.8052657847 0.4662061971 0.8672238389 0.1290994449 0.6846945321 0.5525944225 0.505661094 0.3320823036];
[h, p, ci, stats] = ttest2(grid_2d_minor, grid_3d_minor);
grid_2d_minor_mean = mean(grid_2d_minor);
grid_2d_minor_std = std(grid_2d_minor);
grid_3d_minor_mean = mean(grid_3d_minor);
grid_3d_minor_std = std(grid_3d_minor);
%% ttest2 major and minor axis helical (Grid cells)
grid_3d_major = [5 5 3 5 5 5 5 5 5 5 5 4 5 4 5 5 5 2 5 5 5 5 5 1 5 5 5 5 5 4 5 4 5 5 5 4];
grid_3d_minor = [0.46474 0.551735 0.344095 0.754665 0.517965 0.517155 0.591845 0.4119 0.54633 0.23805 0.76189 0.39096 0.87562 0.452965 0.738285 0.48321 0.462525 0.33785 0.4483907304 0.5714453888 0.8580920657 0.5053760316 0.4947534898 0.3591251 0.438195039 0.6236926937 0.3902599898 0.5803358673 0.8052657847 0.4662061971 0.8672238389 0.1290994449 0.6846945321 0.5525944225 0.505661094 0.3320823036];
[h, p, ci, stats] = ttest2(grid_3d_minor, grid_3d_major);
grid_3d_minor_mean = mean(grid_3d_minor);
grid_3d_minor_std = std(grid_3d_minor);
grid_3d_major_mean = mean(grid_3d_major);
grid_3d_major_std = std(grid_3d_major);
%% ttest2 aspect ratio aspect ratio helical and 2d (grid cells)
grid_3d_aspectR = [10.75870379 9.062321586 8.718522501 6.625456328 9.653161893 9.66828127 8.448157879 12.13886866 9.151977742 21.00399076 6.562627151 10.2312257 5.710239602 8.830704359 6.772452373 10.34746797 10.81022647 5.919786888 11.15098877 8.749742491 5.826880587 9.893623139 10.10604291 2.784544996 11.41044411 8.016768595 12.81197184 8.615700461 6.209130072 8.579894529 5.765524165 30.98386677 7.302526551 9.04822741 9.888045687 12.04520674];
grid_2d_aspectR = [1.214614559 2.70530065 1.288873021 1.860842816 1.145056963 3.300931227 2.670717671 1.38489209 1.102740354 1.835011239 3.649505894 1.238219588 1.276716825 3.019269222 1.475498297 2.800186721 1.55199321 1.719570404 1.608891924 2.006393573 1.766183673 1.255467577 2.413715449 1.288309062 2.845367322 1.5 1 1.678583124 2];
[h, p, ci, stats] = ttest2(grid_3d_aspectR, grid_2d_aspectR);
grid_3d_aspectR_mean = mean(grid_3d_aspectR);
grid_3d_aspectR_std = std(grid_3d_aspectR);
grid_2d_aspectR_mean = mean(grid_2d_aspectR);
grid_2d_aspectR_std = std(grid_2d_aspectR);
%% field extend in coils (Grid cells)
grid_3d_major = [5 5 3 5 5 5 5 5 5 5 5 4 5 4 5 5 5 2 5 5 5 5 5 1 5 5 5 5 5 4 5 4 5 5 5 4];
count5 = sum(grid_3d_major == 5);
count4 = sum(grid_3d_major == 4);
count3 = sum(grid_3d_major == 3);
count2 = sum(grid_3d_major == 2);
count1 = sum(grid_3d_major == 1);
X = [1,2,3,4,5];
sum_count = count1 + count2 + count3 + count4 + count5;
Y = [count1*100/(sum_count), count2*100/(sum_count), count3*100/(sum_count), count4*100/(sum_count), count5*100/(sum_count)];
figure;
p1= bar(X, Y, 'FaceColor','#808080');
%set(p1,'FaceColor','red');
xlabel("Vertical field size (coils)");
ylabel("Percentage fields");
set(gca, 'FontSize', 20);
%% Major and Minor axis length place cells
place_3d_minor = [0.84524 0.553228 0.581896 0.43616 0.704888 0.355072 0.51438 0.546812 0.48892 0.536308 0.257164 1.12132 0.154164 0.046188 0.337916 0.402792 0.349768 0.650408 0.787632 0.336856 0.472176 0.531224 0.444852 0.522744 0.47112 0.55718 0.482044 0.21294 0.3989 0.10328 0.34954 0.34372 0.510324 0.244212 0.569104 0.236196 0.236196 0.939092 0.598516 0.552532 0.409744 0.386288 0.594652 0.477864 0.52892 0.281416 0.551468 0.468632 0.524804 0.21802 0.21802 0.166532 1.179956 0.625804 0.324912 0.4026 0.380872 0.650772 0.768444 0.293868 0.461972 0.497328 0.453156 0.539472 0.409576 0.549128 0.495784 0.391908 0.391372 0.3325 0.344332 0.544868 0.242712 0.5837 0.245676 0.245676];
place_3d_major = [5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 1 5 5 5 3 5 5 5 2 2 1 5 3 5 1 5 1 1 5 5 5 5 4 5 5 5 1 5 5 5 2 1 5 5 5 5 5 5 5 5 1 5 5 5 5 5 5 5 5 4 5 5 5 4 5 1 1];
place_2d_major = [0.7539842639 0.5102592901 0.5385451732 0.3852359872 0.4752721265 0.5068234914 0.3633638894 0.5815490003 0.6434005597 0.5623908832 0.6162457419 0.6010551467 0.6371699586 0.4037417508 0.3440249532 0.2974017314 0.4887507829 0.6720460575 0.3664538995 0.4452491224 0.5390171666 0.510113605 0.6930893318 0.3062640295 0.6566488177 0.1732050808 0.1154700538 0.282099548 0.1154700538];
place_2d_minor = [0.1760485701 0.3229981902 0.5495352998 0.5235088226 0.4103321728 0.2618040259 0.6348144702 0.3818947259 0.2426696942 0.4856625345 0.04618802154 0.3337530245 0.3975651699 0.2342174095 0.07096424943 0.167710531 0.5396179497 0.07779652996 0.07302967433 0.08326663998 0.4420635688 0.04618802154 0.1292714629 0.6348500116 0.3967947356 0.430313642 0.1596428675 0.3864839154 0.07344809129 0.4223801212 0.1110899828 0.6087874189 0.1593915278 0.2190659415 0.3075356453];
place_3d_minor_mean = mean(place_3d_minor);
place_3d_major_mean = mean(place_3d_major);
place_2d_major_mean = mean(place_2d_major);
place_2d_minor_mean = mean(place_2d_minor);
place_3d_minor_std = std(place_3d_minor);
place_3d_major_std = std(place_3d_major);
place_2d_major_std = std(place_2d_major);
place_2d_minor_std = std(place_2d_minor);
std_err_minor = [place_2d_minor_std, place_3d_minor_std];
std_err_major = [place_2d_major_std, place_3d_major_std];
std_err = [std_err_minor; std_err_major];
bar_dat = [place_2d_minor_mean, place_3d_minor_mean; place_2d_major_mean, place_3d_major_mean];
err = [place_2d_minor_std, place_3d_minor_std; place_2d_major_std, place_3d_major_std];
env_type = {'flat arena', 'Helical maze', 'flat arena', 'Helical maze'};
col = [1,1,1; 0.5,0.5,0.5; 1,1,1; 0.5,0.5,0.5];
for bb = 1:4
% bb is bars in bar graph iterator to have different colors
if bb <3
bb
b = bar(0.1 + 0.1*bb, bar_dat(bb),0.1, 'DisplayName',env_type{1,bb}, 'LineWidth', 1.0);
set(b,'FaceColor',col(bb,:))
%legend(b, env_type{1,bb});
%legend(b, env_type{2,bb});
hold on
er = errorbar(0.1 + 0.1*bb ,bar_dat(bb),err(bb),err(bb), 'HandleVisibility','off');
er.Color = [0 0 0];
er.LineWidth = 1.0;
er.LineStyle = 'none';
hold on
else
b = bar(0.15 + 0.1*bb, bar_dat(bb) ,0.1, 'HandleVisibility','off', 'LineWidth', 1.0);
bb
set(b,'FaceColor',col(bb,:))
hold on
er = errorbar(0.15 + 0.1*bb ,bar_dat(bb) ,err(bb),err(bb), 'HandleVisibility','off');
er.Color = [0 0 0];
er.LineWidth = 1.0;
er.LineStyle = 'none';
hold on
end
end
set(gca, 'xtick', [0.25, 0.5])
set(gca, 'xticklabel',{'Minor Axis', 'Major Axis'})
xlim([0.0,0.8]);
legend;
ylabel('Field length (units)');
%% Major and Minor axis length grid cells
grid_3d_minor = [0.46474 0.551735 0.344095 0.754665 0.517965 0.517155 0.591845 0.4119 0.54633 0.23805 0.76189 0.39096 0.87562 0.452965 0.738285 0.48321 0.462525 0.33785 0.4483907304 0.5714453888 0.8580920657 0.5053760316 0.4947534898 0.3591251 0.438195039 0.6236926937 0.3902599898 0.5803358673 0.8052657847 0.4662061971 0.8672238389 0.1290994449 0.6846945321 0.5525944225 0.505661094 0.3320823036];
grid_3d_major = [5 5 3 5 5 5 5 5 5 5 5 4 5 4 5 5 5 2 5 5 5 5 5 1 5 5 5 5 5 4 5 4 5 5 5 4];
grid_2d_major = [0.7539842639 0.5102592901 0.5385451732 0.3852359872 0.4752721265 0.5068234914 0.3633638894 0.5815490003 0.6434005597 0.5623908832 0.6162457419 0.6010551467 0.6371699586 0.4037417508 0.3440249532 0.2974017314 0.4887507829 0.6720460575 0.3664538995 0.4452491224 0.5390171666 0.510113605 0.6930893318 0.3062640295 0.6566488177 0.1732050808 0.1154700538 0.282099548 0.1154700538];
grid_2d_minor = [0.6207601075 0.1886146333 0.4178419166 0.2070223147 0.4150641774 0.1535395488 0.1360547741 0.4199236926 0.5834560761 0.3064781682 0.1688573083 0.4854188646 0.4990691328 0.1337216794 0.2331584889 0.1062078215 0.3149181194 0.3908220658 0.2277678779 0.2219151459 0.3051874927 0.4063136432 0.2871462467 0.2377255883 0.2307782242 0.1154700538 0.1154700538 0.1680581342 0.05773502692];
grid_3d_minor_mean = mean(grid_3d_minor);
grid_3d_major_mean = mean(grid_3d_major);
grid_2d_major_mean = mean(grid_2d_major);
grid_2d_minor_mean = mean(grid_2d_minor);
grid_3d_minor_std = std(grid_3d_minor);
grid_3d_major_std = std(grid_3d_major);
grid_2d_major_std = std(grid_2d_major);
grid_2d_minor_std = std(grid_2d_minor);
std_err_minor = [grid_2d_minor_std, grid_3d_minor_std];
std_err_major = [grid_2d_major_std, grid_3d_major_std];
std_err = [std_err_minor; std_err_major];
bar_dat = [grid_2d_minor_mean, grid_3d_minor_mean; grid_2d_major_mean, grid_3d_major_mean];
err = [grid_2d_minor_std, grid_3d_minor_std; grid_2d_major_std, grid_3d_major_std];
env_type = {'flat arena', 'Helical maze', 'flat arena', 'Helical maze'};
col = [1,1,1; 0.5,0.5,0.5; 1,1,1; 0.5,0.5,0.5];
for bb = 1:4
% bb is bars in bar graph iterator to have different colors
if bb <3
bb
b = bar(0.1 + 0.1*bb, bar_dat(bb),0.1, 'DisplayName',env_type{1,bb}, 'LineWidth', 1.0);
set(b,'FaceColor',col(bb,:))
%legend(b, env_type{1,bb});
%legend(b, env_type{2,bb});
hold on
er = errorbar(0.1 + 0.1*bb ,bar_dat(bb),err(bb),err(bb), 'HandleVisibility','off');
er.Color = [0 0 0];
er.LineWidth = 1.0;
er.LineStyle = 'none';
hold on
else
b = bar(0.15 + 0.1*bb, bar_dat(bb) ,0.1, 'HandleVisibility','off', 'LineWidth', 1.0);
bb
set(b,'FaceColor',col(bb,:))
hold on
er = errorbar(0.15 + 0.1*bb ,bar_dat(bb) ,err(bb),err(bb), 'HandleVisibility','off');
er.Color = [0 0 0];
er.LineWidth = 1.0;
er.LineStyle = 'none';
hold on
end
end
set(gca, 'xtick', [0.25, 0.5])
set(gca, 'xticklabel',{'Minor Axis', 'Major Axis'})
xlim([0.0,0.8]);
legend;
ylabel('Field length (units)');
%% Aspect ratio plot grid
grid_3d_aspectR = [10.75870379 9.062321586 8.718522501 6.625456328 9.653161893 9.66828127 8.448157879 12.13886866 9.151977742 21.00399076 6.562627151 10.2312257 5.710239602 8.830704359 6.772452373 10.34746797 10.81022647 5.919786888 11.15098877 8.749742491 5.826880587 9.893623139 10.10604291 2.784544996 11.41044411 8.016768595 12.81197184 8.615700461 6.209130072 8.579894529 5.765524165 30.98386677 7.302526551 9.04822741 9.888045687 12.04520674];
grid_2d_aspectR = [1.214614559 2.70530065 1.288873021 1.860842816 1.145056963 3.300931227 2.670717671 1.38489209 1.102740354 1.835011239 3.649505894 1.238219588 1.276716825 3.019269222 1.475498297 2.800186721 1.55199321 1.719570404 1.608891924 2.006393573 1.766183673 1.255467577 2.413715449 1.288309062 2.845367322 1.5 1 1.678583124 2];
grid_3d_aspectR_mean = mean(grid_3d_aspectR);
grid_2d_aspectR_mean = mean(grid_2d_aspectR);
grid_3d_aspectR_std = std(grid_3d_aspectR);
grid_2d_aspectR_std = std(grid_2d_aspectR);
bar_dat = [grid_2d_aspectR_mean; grid_3d_aspectR_mean];
err = [grid_2d_aspectR_std; grid_3d_aspectR_std];
env_type = {'flat arena', 'Helical maze'};
col = [1,1,1; 0.5,0.5,0.5];
for bb = 1:2
% bb is bars in bar graph iterator to have different colors
if bb < 2
bb
b = bar(0.1 + 0.1*bb, bar_dat(bb),0.1, 'DisplayName',env_type{1,bb}, 'LineWidth', 1.0);
set(b,'FaceColor',col(bb,:))
hold on
er = errorbar(0.1 + 0.1*bb ,bar_dat(bb),err(bb),err(bb), 'HandleVisibility','off');
er.Color = [0 0 0];
er.LineWidth = 1.0;
er.LineStyle = 'none';
hold on
else
b = bar(0.15 + 0.1*bb, bar_dat(bb) ,0.1, 'DisplayName',env_type{1,bb}, 'LineWidth', 1.0);
bb
set(b,'FaceColor',col(bb,:))
hold on
er = errorbar(0.15 + 0.1*bb ,bar_dat(bb) ,err(bb),err(bb), 'HandleVisibility','off');
er.Color = [0 0 0];
er.LineWidth = 1.0;
er.LineStyle = 'none';
hold on
end
end
set(gca, 'xtick', [0.2; 0.35])
set(gca, 'xticklabel',{'Flat arena', 'Helical maze'})
xlim([0.0,0.5]);
legend;
ylabel('Aspect ratio');
%% Aspect ratio plot place
place_3d_aspectR = [5.915479627 9.037865039 8.59260074 11.46368305 7.093325464 14.08165105 9.720440142 9.143910521 10.22662194 9.323000962 19.44284581 4.459030428 32.43299344 108.2532259 14.79657666 12.41335478 14.29518995 7.687482319 6.34814228 2.968627544 10.5892718 9.412225351 11.2396932 5.738946788 10.6130073 8.973760724 10.37249712 9.392317085 5.013787917 9.682416731 14.3045145 8.728034447 9.797697149 4.094802876 8.785740392 4.233771952 4.233771952 5.324291976 8.353995549 9.049249636 12.20274122 12.94371039 6.726623302 10.46322803 9.453225441 17.76729113 1.813341844 10.6693525 9.527366407 22.93367581 9.173470324 6.00485192 4.237446142 7.989722022 15.38878219 12.41927471 13.12776996 7.683182436 6.506655007 17.01444186 2.164633354 10.05372712 11.0337279 9.268321618 12.20774655 9.105345202 10.08503703 12.75809629 12.77556902 12.03007519 14.52086939 9.1765345 20.60054715 6.852835361 20.35200834 4.070401667];
place_2d_aspectR = [2.904928466 2.475974833 1.415131231 1.527976687 1.439957401 1.127139174 1.092725463 1.416433403 2.058418221 1.154840966 2 1.923112226 1.421609739 1.283074299 2.809996831 2.426163615 1.441112266 3.933868321 2 1.467598771 1.262814562 4 1.82185316 1.108666796 1.78749679 1.272893473 3.071448571 1.359898364 3.003033072 1.492775262 3.119286799 1.142316185 2.525470603 2.576393719 1.843020881];
place_3d_aspectR_mean = mean(place_3d_aspectR);
place_2d_aspectR_mean = mean(place_2d_aspectR);
place_3d_aspectR_std = std(place_3d_aspectR);
place_2d_aspectR_std = std(place_2d_aspectR);
bar_dat = [place_2d_aspectR_mean; place_3d_aspectR_mean];
err = [place_2d_aspectR_std; place_3d_aspectR_std];
figure;
hold on;
env_type = {'flat arena', 'Helical maze'};
col = [1,1,1; 0.5,0.5,0.5];
for bb = 1:2
% bb is bars in bar graph iterator to have different colors
if bb < 2
bb
b = bar(0.1 + 0.1*bb, bar_dat(bb),0.1, 'DisplayName',env_type{1,bb}, 'LineWidth', 1.0);
set(b,'FaceColor',col(bb,:))
hold on;
er = errorbar(0.1 + 0.1*bb ,bar_dat(bb),err(bb),err(bb), 'HandleVisibility','off');
er.Color = [0 0 0];
er.LineWidth = 1.0;
er.LineStyle = 'none';
%legend(env_type{1, bb})
%hold on
else
b = bar(0.15 + 0.1*bb, bar_dat(bb), 0.1, 'DisplayName', env_type{1, bb}, 'LineWidth', 1.0);
bb
set(b,'FaceColor',col(bb,:))
hold on;
er = errorbar(0.15 + 0.1*bb ,bar_dat(bb) ,err(bb),err(bb), 'HandleVisibility','off');
er.Color = [0 0 0];
er.LineWidth = 1.0;
er.LineStyle = 'none';
%legend(env_type{1, bb})
hold on
end
end
set(gca, 'xtick', [0.2; 0.35])
set(gca, 'xticklabel',{'Flat arena', 'Helical maze'})
xlim([0.0,0.5]);
legend(env_type, 'Location', 'northwest');
%legend('flat arena','helical maze');
ylabel('Aspect ratio');