bachelor_thesis/DataAnalysisToolbox/reviewSpikeAmplitude.m

%% Script to review the spike amplitude using means and sds
% This script calculates average values of the spike amplitudes for
% different groups that were stated in the analysis. To evaluate the
% consistency of the groups and the spike amplitude it self standard
% deviations are reviewed. All results are displayed in the command window
% with a clear layout.
% -------------------------------------------------------------------------
% Program by: Bjarne Schultze       [last modified: 08.03.2022]
% -------------------------------------------------------------------------

% load the deanonymization file
load("../AdditionalFiles/deanonymization.mat")

% get the numbers of the cells in each package
pack_1_3 = find(eq(deanonymization.package(:,1),13));
pack_2 = find(eq(deanonymization.package(:,1),2));
pack_4_6 = find(eq(deanonymization.package(:,1),46));
pack_5 = find(eq(deanonymization.package(:,1),5));

% take the assigned cell types into account
int218 = find(eq(deanonymization.cellType(:,1),218));
int162 = find(eq(deanonymization.cellType(:,1),162));
int264 = find(eq(deanonymization.cellType(:,1),264));
int212 = find(eq(deanonymization.cellType(:,1),212));
int201203 = find(eq(deanonymization.cellType(:,1),201203));
int159 = find(eq(deanonymization.cellType(:,1),159));
int157 = find(eq(deanonymization.cellType(:,1),157));
int6061 = find(eq(deanonymization.cellType(:,1),6061));

% obtian the spike amplitudes and the standard deviations (the latter are
% not included in the decisionData file)
[spike_heights,spk_hghts_SD] = intSpikeHeight(1:62);
% remove measurements for the interneurons without spikes
spike_heights([5,10,26,36,38,40],1) = NaN;
spk_hghts_SD([5,10,26,36,38,40],1) = NaN;

% define the three groups for the spike amplitudes: small, medium, large
smallSpikers = find(spike_heights < 9);
mediumSpikers = find(spike_heights >= 9 & spike_heights < 30);
largeSpikers = find(spike_heights >= 30);

% display an overview of the central tendencies for the whole dataset and
% for the three single spike amplitude groups. The sd gives the standard
% deviation of the spike amplitude within the current group. This is an
% estimation of how consistent the groups are regarding the spike amplitude
spikeAmpGroups = ...
    sprintf("\nCentral tendencies of the spike amplitude \n" + ...
    "(non-spiking interneurons excluded, mean \x00B1 sd): \n" + ...
    "\tAll: %0.2f mV (mean),  %0.2f mV (median) \n" + ...
    "\tSmall spikers: \t%05.2f \x00B1 %0.2f mV \n" + ...
    "\tMedium spikers: %0.2f \x00B1 %0.2f mV \n" + ...
    "\tLarge spikers: \t%0.2f \x00B1 %0.2f mV", ...
    mean(spike_heights,'omitnan'), median(spike_heights,'omitnan'), ...
    mean(spike_heights(smallSpikers),'omitnan'),...
    std(spike_heights(smallSpikers),'omitnan'), ...
    mean(spike_heights(mediumSpikers),'omitnan'), ...
    std(spike_heights(mediumSpikers),'omitnan'), ...
    mean(spike_heights(largeSpikers),'omitnan'), ...
    std(spike_heights(largeSpikers),'omitnan'));
disp(spikeAmpGroups)

% display an overview of the standard deviations of the spike amplitudes of
% each single neuron. Spike amplitude deviations are averaged for the
% stated groups and give an estimation about how constant the spike
% amplitude was for one cell.
sd_spikeAmpNeurons = sprintf("\nStandard deviations of the spike " + ...
    "amplitude measured for single cells and then averaged for the " + ...
    "stated groups \n(non-spiking interneurons excluded): \n" + ...
    "\tAll: \t\t\t%0.2f mV \n" + ...
    "\tSmall spikers: \t%0.2f mV\n" + ...
    "\tMedium spikers: %0.2f mV \n" + ...
    "\tLarge spikers: \t%0.2f mV \n" + ...
    "\tSmall and medium spikers: %0.2f mV", ...
    mean(spk_hghts_SD, 'omitnan'), ...
    mean(spk_hghts_SD(smallSpikers),'omitnan'), ...
    mean(spk_hghts_SD(mediumSpikers),'omitnan'), ...
    mean(spk_hghts_SD(largeSpikers),'omitnan'),...
    mean(spk_hghts_SD([smallSpikers;mediumSpikers]),'omitnan'));
disp(sd_spikeAmpNeurons)

% create an overview about the average spike amplitude for the single
% interneuron cell types as they were assigned based on size and location
% in the ganglion. Sds are within those groups
spikeAmpNeurons = sprintf("\nAverage spike amplitudes for the " + ...
    "assigned cell types \n(non-spiking interneurons excluded, " + ...
    "mean \x00B1 sd) \n" + ...
    "\t Int 60-61: \t%05.2f \x00B1 %05.2f mV \n" + ...
    "\t Int 157: \t\t%05.2f \x00B1 %05.2f mV \n" + ...
    "\t Int 159: \t\t%05.2f \x00B1 %05.2f mV \n" + ...
    "\t Int 162: \t\t%05.2f \x00B1 %05.2f mV \n" + ...
    "\t Int 201-203: \t%05.2f \x00B1 %05.2f mV \n" + ...
    "\t Int 212: \t\t%05.2f \x00B1 %05.2f mV \n" + ...
    "\t without the two large spikers: \n" + ...
    "\t\t\t\t\t%05.2f \x00B1 %05.2f mV \n" + ...
    "\t Int 218: \t\t%05.2f \x00B1 %05.2f mV \n" + ...
    "\t including the two large spikers labelled as 212: \n" + ...
    "\t\t\t\t\t%05.2f \x00B1 %05.2f mV \n" + ...
    "\t Int 264: \t\t%05.2f \x00B1 %05.2f mV", ...
    mean(spike_heights(int6061),'omitnan'), ...
    std(spike_heights(int6061),'omitnan'), ...
    mean(spike_heights(int157),'omitnan'), ...
    std(spike_heights(int157),'omitnan'), ...
    mean(spike_heights(int159),'omitnan'), ...
    std(spike_heights(int159),'omitnan'), ...
    mean(spike_heights(int162),'omitnan'), ...
    std(spike_heights(int162),'omitnan'), ...
    mean(spike_heights(int201203),'omitnan'), ...
    std(spike_heights(int201203),'omitnan'), ...
    mean(spike_heights(int212),'omitnan'), ...
    std(spike_heights(int212),'omitnan'), ...
    mean(spike_heights(int212([2:5,7:11])),'omitnan'), ...
    std(spike_heights(int212([2:5,7:11])),'omitnan'), ...
    mean(spike_heights(int218),'omitnan'), ...
    std(spike_heights(int218),'omitnan'), ...
    mean(spike_heights([int218;int212([1,6])]),'omitnan'), ...
    std(spike_heights([int218;int212([1,6])]),'omitnan'), ...
    mean(spike_heights(int264),'omitnan'), ...
    std(spike_heights(int264),'omitnan'));
disp(spikeAmpNeurons)

%% End
% clear workspace
clear