-
Notifications
You must be signed in to change notification settings - Fork 0
/
plot_signal_quality_across_sessions.asv
150 lines (118 loc) · 6.37 KB
/
plot_signal_quality_across_sessions.asv
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
function fig = plot_signal_quality_across_sessions(para, sessions_summary)
%% plot params
plot_dayNum = true; % determines whether to plot data against date or session number
titleFontSize=16;
faceAlpha = 0.15;
accuracy_ylims = [0.2 1];
plot_only_ephys_sessions = true;
% load ephys metadata (previously calculated in spikeinterface)
filename = strcat('quality_metrics_KS3_metadata_', para.Animal_ID, '.csv');
output_folder = fullfile(para.output_folder, 'ephys_signal_quality');
%% Append ephys and behavioural session summaries
sessions_summary_ephys = readtable(fullfile(output_folder, filename));
% Convert session ID collumns to strings to allow concatenation of
% tables
sessions_summary.Session_ID = string(sessions_summary.Session_ID);
sessions_summary_ephys.Session_ID = string(sessions_summary_ephys.Session_ID);
% append to sessions summary
sessions_summary = outerjoin(sessions_summary, sessions_summary_ephys, 'Keys', 'Session_ID', 'MergeKeys', true);
% Remove sessions without ephys data (if plot_only_ephys_sessions set
% to True).
if plot_only_ephys_sessions
sessions_summary((sessions_summary.referenceChannel==""),:)=[];
end
%% configure plot layout
fig = figure('Visible','on', 'Position', [278 79 1260 883]);
tl = tiledlayout(3,1);
tl.Padding = "compact";
Animal_ID = sessions_summary.Animal_ID{1,1};
title(tl,[strcat("Mouse ", Animal_ID, " Session Summary Data") ""], "FontSize", titleFontSize+2);
xlabel(tl, 'Days since training started', "FontSize",titleFontSize);
% Get indeces of stage progressions
Stage = cell2mat(sessions_summary.Stage);
changeIdx = ~(Stage - [0;Stage(1:end-1)])==0;
changeIdx = find(changeIdx);
% define x-axis data
if plot_dayNum
dayNum = (sessions_summary.Session_ID');
dayNum = datenum(dayNum, 'yyyy-mm-dd');
dayNum = dayNum-dayNum(1);
x = dayNum;
else
x = 1:height(sessions_summary);
x = x';
end
ephys_recording_bank1 = (sessions_summary.electrodeConfiguration=="All Shanks 1-96");
ephys_recording_bank2 = (sessions_summary.electrodeConfiguration=="All Shanks 97-192");
ephys_recording_bank3 = (sessions_summary.electrodeConfiguration=="All Shanks 193-288");
ephys_recording_bank4 = (sessions_summary.electrodeConfiguration=="All Shanks 289-384");
%% plot behaviour performance across days
ax1 = nexttile;
hold on;
title(ax1, 'Plot performance over days of training', 'FontSize',titleFontSize)
% plot accuracy of all non-aborted trials
pl1 = plot_shaded_error_bar(x, sessions_summary.accuracy_completed_trials, ...
sessions_summary.accuracy_completed_trials_bpci, para.colour_accuracy, faceAlpha);
pl2 = plot(x, sessions_summary.accuracy_all_trials, 'LineWidth', 2, 'Color', ...
para.colour_accuracy, 'LineStyle','--');
yline(0.5, '--', "LineWidth",1);
yline(0.7, ':', "LineWidth",1);
% mark recording banks for sessions with ephys data
pl3 = mark_condition(x,sessions_summary.accuracy_completed_trials, ...
ephys_recording_bank1,para.colour_accuracy,'square',70);
pl4 = mark_condition(x,sessions_summary.accuracy_completed_trials, ...
ephys_recording_bank2,para.colour_accuracy,'o',50);
pl5 = mark_condition(x,sessions_summary.accuracy_completed_trials, ...
ephys_recording_bank3,para.colour_accuracy,'diamond',50);
pl6 = mark_condition(x,sessions_summary.accuracy_completed_trials, ...
ephys_recording_bank4,para.colour_accuracy,'^',50);
% mark any stage progressions
for i = 1:length(changeIdx)
StageStr = strcat("Stage ",num2str(Stage(changeIdx(i))));
xline(changeIdx(i), '--', StageStr, 'FontSize',titleFontSize-4);
end
ylim(accuracy_ylims)
xlim([min(x) max(x)]);
ylabel('Fraction of Correct Trials', "FontSize",titleFontSize);
legend([pl1 pl2 pl3 pl4 pl5 pl6], {'Fraction of Completed Trials', 'Fraction of All Trials', ...
'Recording Bank 1', 'Recording Bank 2', 'Recording Bank 3', 'Recording Bank 4'}, ...
'FontSize', titleFontSize, 'Location','eastoutside');
% plot dataset size across days
ax2 = nexttile;
hold on
title('Plot dataset size over days of training', 'FontSize', titleFontSize);
% mark any stage progressions
for i = 1:length(changeIdx)
StageStr = strcat("Stage ",num2str(Stage(changeIdx(i))));
xline(changeIdx(i), '--', StageStr, 'FontSize',titleFontSize-4);
end
yyaxis left
pl1 = plot(dayNum, sessions_summary.numTrialsCompleted, ...
'LineWidth', 2, ...
'Color', [0.8500 0.3250 0.0980]);
ylabel('Number of trials completed', 'FontSize',titleFontSize, ...
'Color',[0.8500 0.3250 0.0980]);
yyaxis right
pl2 = plot(dayNum, sessions_summary.num_units, ...
'Linewidth' , 2, ...
'Color',[0 0.4470 0.7410]);
ylabel('Number of units', 'FontSize',titleFontSize)
% plot ephys data quality across days
ax3 = nexttile;
hold on
title('Plot ephys quality metrics over days of training', 'FontSize', titleFontSize);
% mark any stage progressions
for i = 1:length(changeIdx)
StageStr = strcat("Stage ",num2str(Stage(changeIdx(i))));
xline(changeIdx(i), '--', StageStr, 'FontSize',titleFontSize-4);
end
pl1 = plot(dayNum, sessions_summary.l_ratio_median./max(sessions_summary.l_ratio_median), ...
'LineWidth',2, 'Color',[0.4940 0.1840 0.5560]);
pl2 = plot(dayNum, sessions_summary.isolation_distance_median./max(sessions_summary.isolation_distance_median), ...
'LineWidth',2, 'Color',[0.3010 0.7450 0.9330]);
pl3 = plot(dayNum, sessions_summary.d_prime_median, ...
'LineWidth',2, 'Color',[0.9290 0.6940 0.1250]);
legend([pl1 pl2 pl3], {'normalised median L-ratio', 'normalised median isolation distance', ...
'median d-prime'}, 'FontSize', titleFontSize, 'Location','eastoutside');
linkaxes([ax1 ax2 ax3], 'x');
end