-
Notifications
You must be signed in to change notification settings - Fork 0
/
m3_TD_Ratio.m
278 lines (234 loc) · 10.3 KB
/
m3_TD_Ratio.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
% Calculate and save average length of state, number of state changes, and
% ratio of HTD to LTD. Run 1-way and 2-way ANOVAs
% Load relevant reference data
load('SpkInfo.mat')
% Initialize labels for ANOVA testing
nStroke = cell(1,40);
nEE = cell(1,40);
lltdStroke = cell(1,239);
lltdEE = cell(1,239);
rltdStroke = cell(1,263);
rltdEE = cell(1,263);
rltdStroke = cell(1,263);
rltdEE = cell(1,263);
lhtdStroke = cell(1,279);
lhtdEE = cell(1,279);
rhtdStroke = cell(1,303);
rhtdEE = cell(1,303);
[nStroke,nEE] = labelMaker(9,0,nStroke,nEE,'Control','Std');
[nStroke,nEE] = labelMaker(10,9,nStroke,nEE,'Control','EE');
[nStroke,nEE] = labelMaker(11,19,nStroke,nEE,'Stroke','Std');
[nStroke,nEE] = labelMaker(10,30,nStroke,nEE,'Stroke','EE');
[lltdStroke,lltdEE] = labelMaker(28,0,lltdStroke,lltdEE,'Control','Std');
[lltdStroke,lltdEE] = labelMaker(53,28,lltdStroke,lltdEE,'Control','EE');
[lltdStroke,lltdEE] = labelMaker(76,81,lltdStroke,lltdEE,'Stroke','Std');
[lltdStroke,lltdEE] = labelMaker(82,157,lltdStroke,lltdEE,'Stroke','EE');
[lhtdStroke,lhtdEE] = labelMaker(37,0,lhtdStroke,lhtdEE,'Control','Std');
[lhtdStroke,lhtdEE] = labelMaker(63,37,lhtdStroke,lhtdEE,'Control','EE');
[lhtdStroke,lhtdEE] = labelMaker(87,100,lhtdStroke,lhtdEE,'Stroke','Std');
[lhtdStroke,lhtdEE] = labelMaker(92,187,lhtdStroke,lhtdEE,'Stroke','EE');
[rhtdStroke,rhtdEE] = labelMaker(42,0,rhtdStroke,rhtdEE,'Control','Std');
[rhtdStroke,rhtdEE] = labelMaker(60,42,rhtdStroke,rhtdEE,'Control','EE');
[rhtdStroke,rhtdEE] = labelMaker(111,102,rhtdStroke,rhtdEE,'Stroke','Std');
[rhtdStroke,rhtdEE] = labelMaker(90,213,rhtdStroke,rhtdEE,'Stroke','EE');
[rltdStroke,rltdEE] = labelMaker(33,0,rltdStroke,rltdEE,'Control','Std');
[rltdStroke,rltdEE] = labelMaker(50,33,rltdStroke,rltdEE,'Control','EE');
[rltdStroke,rltdEE] = labelMaker(100,83,rltdStroke,rltdEE,'Stroke','Std');
[rltdStroke,rltdEE] = labelMaker(80,183,rltdStroke,rltdEE,'Stroke','EE');
% Initialize counter for inserting data correctly for anova testing
counter = 0;
for i = 1:4
results1way(i).lNum = [];
results1way(i).lHtd = [];
results1way(i).lLtd = [];
results1way(i).lR = [];
results1way(i).rNum = [];
results1way(i).rHtd = [];
results1way(i).rLtd = [];
results1way(i).rR = [];
end
results2way.lNum = [];
results2way.lHtd = [];
results2way.lLtd = [];
results2way.lR = [];
results2way.rNum = [];
results2way.rHtd = [];
results2way.rLtd = [];
results2way.rR = [];
% Pull and process data
for group = [3 6 8 7 10]
% 1.Load the right and left side signals
% load H/L TD indexes
switch group
case 3
new_group = 1;
case 6
new_group = 2;
case 8
new_group = 3;
case 7
new_group = 4;
case 10
new_group = 6;
end
for animal = 1: length(SpkInfo{group,2})
% Define filepath to pull from
REM = ['C:\Users\ipzach\Documents\MATLAB\Data\Chronic Stroke' filesep SpkInfo{group,1} '_' num2str(animal) filesep 'cREM.mat'];
% Error checking and exceptions for missing files
try
load(REM);
catch
disp('Rem not loaded')
continue
end
if isempty(cREM.R.start) || isempty(cREM.R.end)
disp('Missing REM Start or End Times for Right Side')
cd ..
continue
end
if isempty(cREM.L.start) || isempty(cREM.L.end)
disp('Missing REM Start or End Times for Left Side')
cd ..
continue
end
% REM loaded correctly, process
% 2way ANOVA
% only handle controls and 1MS groups
if new_group == 1 || new_group == 2 || new_group == 3 || new_group == 6
results2way = analyze(cREM.R, results2way, 'R');
results2way = analyze(cREM.L, results2way, 'L');
end
% 1way ANOVA
% only handle non EE groups
if new_group == 1 || new_group == 3 || new_group == 4
results1way(new_group) = analyze(cREM.R, results1way(new_group), 'R');
results1way(new_group) = analyze(cREM.L, results1way(new_group), 'L');
end
end % animal
end % group
reset = pwd;
cd('C:\Users\ipzach\Documents\MATLAB\output\Stats');
save('Raw Vals', 'results1way','results2way');
cd(reset)
disp('saved')
% ONE WAY ANOVA
lHtd = NaN(87,3);
lHtd(1:length(results1way(1).lHtd),1) = results1way(1).lHtd;
lHtd(1:length(results1way(4).lHtd),2) = results1way(4).lHtd;
lHtd(1:length(results1way(3).lHtd),3) = results1way(3).lHtd;
rHtd = NaN(111,3);
rHtd(1:length(results1way(1).rHtd),1) = results1way(1).rHtd;
rHtd(1:length(results1way(4).rHtd),2) = results1way(4).rHtd;
rHtd(1:length(results1way(3).rHtd),3) = results1way(3).rHtd;
rLtd = NaN(100,3);
rLtd(1:length(results1way(1).rLtd),1) = results1way(1).rLtd;
rLtd(1:length(results1way(4).rLtd),2) = results1way(4).rLtd;
rLtd(1:length(results1way(3).rLtd),3) = results1way(3).rLtd;
lLtd = NaN(76,3);
lLtd(1:length(results1way(1).lLtd),1) = results1way(1).lLtd;
lLtd(1:length(results1way(4).lLtd),2) = results1way(4).lLtd;
lLtd(1:length(results1way(3).lLtd),3) = results1way(3).lLtd;
lNum = NaN(11,3);
lNum(1:length(results1way(1).lNum),1) = results1way(1).lNum;
lNum(1:length(results1way(4).lNum),2) = results1way(4).lNum;
lNum(1:length(results1way(3).lNum),3) = results1way(3).lNum;
rNum = NaN(11,3);
rNum(1:length(results1way(1).rNum),1) = results1way(1).rNum;
rNum(1:length(results1way(4).rNum),2) = results1way(4).rNum;
rNum(1:length(results1way(3).rNum),3) = results1way(3).rNum;
lR = NaN(11,3);
lR(1:length(results1way(1).lR),1) = results1way(1).lR;
lR(1:length(results1way(4).lR),2) = results1way(4).lR;
lR(1:length(results1way(3).lR),3) = results1way(3).lR;
rR = NaN(11,3);
rR(1:length(results1way(1).rR),1) = results1way(1).rR;
rR(1:length(results1way(4).rR),2) = results1way(4).rR;
rR(1:length(results1way(3).rR),3) = results1way(3).rR;
labels = {'Ctrl','2WS','1MS'};
[~,~,lHtdS1] = anova1(lHtd, labels,'off');
[~,~,lLtdS1] = anova1(lLtd, labels,'off');
[~,~,rHtdS1] = anova1(rHtd, labels,'off');
[~,~,rLtdS1] = anova1(rLtd,labels,'off');
[~,~,lNumS1] = anova1(lNum, labels,'off');
[~,~,rNumS1] = anova1(rNum, labels,'off');
[~,~,lRS1] = anova1(lR, labels,'off');
[~,~,rRS1] = anova1(rR, labels,'off');
[lHtdC1,lHtdM1,~,lHtdN1] = multcompare(lHtdS1,'CType','bonferroni','Display','off');
[lLtdC1,lLtdM1,~,lLtdN1] = multcompare(lLtdS1,'CType','bonferroni','Display','off');
[rHtdC1,rHtdM1,~,rHtdN1] = multcompare(rHtdS1,'CType','bonferroni','Display','off');
[rLtdC1,rLtdM1,~,rLtdN1] = multcompare(rLtdS1,'CType','bonferroni','Display','off');
[lNumC1,lNumM1,~,lNumN1] = multcompare(lNumS1,'CType','bonferroni','Display','off');
[rNumC1,rNumM1,~,rNumN1] = multcompare(rNumS1,'CType','bonferroni','Display','off');
[lRC1,lRM1,~,lRN1] = multcompare(lRS1,'CType','bonferroni','Display','off') ;
[rRC1,rRM1,~,rRN1] = multcompare(rRS1,'CType','bonferroni','Display','off') ;
% % TWO WAY ANOVA
[~,alHtdT2,lHtdS2] = anovan(results2way.lHtd, {lhtdStroke,lhtdEE},'model','interaction','display','off');
[~,alLtdT2,lLtdS2] = anovan(results2way.lLtd, {lltdStroke,lltdEE},'model','interaction','display','off');
[~,arHtdT2,rHtdS2] = anovan(results2way.rHtd, {rhtdStroke,rhtdEE},'model','interaction','display','off');
[~,arLtdT2,rLtdS2] = anovan(results2way.rLtd, {rltdStroke,rltdEE},'model','interaction','display','off');
[~,alNumT2,lNumS2] = anovan(results2way.lNum, {nStroke,nEE},'model','interaction','display','off');
[~,arNumT2,rNumS2] = anovan(results2way.rNum, {nStroke,nEE},'model','interaction','display','off');
[~,alRT2,lRS2] = anovan(results2way.lR, {nStroke,nEE},'model','interaction','display','off');
[~,arRTs,rRS2] = anovan(results2way.rR, {nStroke,nEE},'model','interaction','display','off');
[lHtdC2,lHtdM2,~,lHtdN2] = multcompare(lHtdS2,'dimension',[1 2],'CType','bonferroni','Display','off');
[lLtdC2,lLtdM2,~,lLtdN2] = multcompare(lLtdS2,'dimension',[1 2],'CType','bonferroni','Display','off');
[rHtdC2,rHtdM2,~,rHtdN2] = multcompare(rHtdS2,'dimension',[1 2],'CType','bonferroni','Display','off');
[rLtdC2,rLtdM2,~,rLtdN2] = multcompare(rLtdS2,'dimension',[1 2],'CType','bonferroni','Display','off');
[lNumC2,lNumM2,~,lNumN2] = multcompare(lNumS2,'dimension',[1 2],'CType','bonferroni','Display','off');
[rNumC2,rNumM2,~,rNumN2] = multcompare(rNumS2,'dimension',[1 2],'CType','bonferroni','Display','off');
[lRC2,lRM2,~,lRN2] = multcompare(lRS2,'dimension',[1 2],'CType','bonferroni','Display','off');
[rRC2,rRM2,~,rRN2] = multcompare(rRS2,'dimension',[1 2],'CType','bonferroni','Display','off');
disp('Saving...')
save('C:\Users\user\Documents\MATLAB\Stats\State\FullStats.mat',...
'lHtdC2','lHtdM2','lHtdN2','lLtdC2','lLtdM2','lLtdN2','rHtdC2','rHtdM2','rHtdN2',...
'rLtdC2','rLtdM2','rLtdN2','lNumC2','lNumM2','lNumN2','rNumC2','rNumM2','rNumN2',...
'lRC2','lRM2','lRN2','rRC2','rRM2','rRN2','lHtdC1','lHtdM1','lHtdN1',...
'lLtdC1','lLtdM1','lLtdN1','rHtdC1','rHtdM1','rHtdN1','rLtdC1','rLtdM1','rLtdN1',...
'lNumC1','lNumM1','lNumN1','rNumC1','rNumM1','rNumN1','lRC1','lRM1','lRN1',...
'rRC1','rRM1','rRN1');
disp('HAH! GOTEEEM')
function [d] = analyze(times,d,side)
% This function takes in a struct with two fields, start and end
% and calculates length of state (HTD), ratio of HTD to LTD, and
% number of states
% initialize state length storage variables
htd = [];
ltd = [];
% Calculate state length
for iT = 1:length(times.start)
% subtract end time (i) from start time (i) to find each length
% of on state
htd = [htd (times.end(iT)-times.start(iT))];
% subtract start time (i) from end time (i-1) to find each length
% of off state. At i = 1, start at 0.
if iT == 1
ltd = ltd + times.start(iT);
else
ltd = [ltd (times.start(iT) - times.end(iT-1))];
end
end
perc = sum(htd)/(sum(htd)+sum(ltd));
if length(times.start) == length(times.end)
s = length(times.start);
else
disp('Start and end lengths differ');
end
switch side
case 'L'
d.lNum = [d.lNum s];
d.lHtd = [d.lHtd htd];
d.lLtd = [d.lLtd ltd];
d.lR = [d.lR perc];
case 'R'
d.rNum = [d.rNum s];
d.rHtd = [d.rHtd htd];
d.rLtd = [d.rLtd ltd];
d.rR = [d.rR perc];
end
end
function [stroke,EE] = labelMaker(lim,prev,stroke,EE,label,treatment)
for i = 1:lim
stroke{prev+i} = label;
EE{prev+i} = treatment;
end
end