tsne_on_human_group_genes_average_perplexity_sweep_2D.m

%% Perform Barnes-Hut t-SNE on mouse gene data
clear variables
close all

addpath('../bh-tsne');
ids = {'9861','10021','12876','14380','15496','15697'};
nbrains = length(ids);

% initial_dims_vec = [2 3 5 10:10:100];
initial_dims_vec = [1 2 3 4 5 6 10:10:100];
initial_dims_vec = [7 8 9];
initial_dims_vec = [];
perplexity_vec = 2.^(1:10);
% initial_dims_vec = 100;
nperp = length(perplexity_vec);

%% Load data
X = [];
coords = [];
color_RGB = [];
structure_id = [];
brain_id = [];
for bnr = 1:nbrains
    id = ids{bnr};
    datadir = ['/home/mvandegiessen/data/tSNE_ABA/rawData_25Feb2014/normalized_microarray_donor' id '/'];
    outdir = 'results_human_average_perplexity_sweep/';
    expressionlevels = load([datadir 'geneMicroarrayExpression']);
    
    %     % Load gene selection
    %     if bnr == 1
    %         indexdata = load([datadir 'probe2gene_index']);
    %         allgindices = 1:size(expressionlevels.MicroarrayExpression,1);
    %         selprobes = allgindices(indexdata.probe2gene_index>0);
    %     end
    
    % Load gene coordinates, color, structure_ID
    sampledata = load([datadir 'sample']);
    coords = [coords; [sampledata.sample.mni_x,sampledata.sample.mni_y,sampledata.sample.mni_z]];
    color_RGB = [color_RGB; sampledata.sample.color_RGB];
    structure_id = [structure_id; sampledata.sample.structure_id];
    brain_id = [brain_id; bnr*ones(length(sampledata.sample.mni_x),1)];
    
    % Normalize data
    Xnew = expressionlevels.geneMicroarrayExpression';
    %     meanXnew = mean(Xnew,2);
    %     stdXnew = std(Xnew,[],2);
    %     Xnew = bsxfun(@minus,Xnew,meanXnew);
    %     Xnew = bsxfun(@rdivide,Xnew,stdXnew);
    % Per gene
    Xnew = zscore(Xnew,0,1);
    % Per brain
%     Xnew = zscore(Xnew,0,2);
    
    % Data subselection
    X = [X; Xnew];
end
X0 = X;

%% Perform t-SNE
for pnr = 1:nperp
    X = X0;
    
    % selvec = randperm(size(X,1));
    selvec = 1:size(X,1);
    X = X(selvec,:);
    coords = coords(selvec,:);
    perplexity = perplexity_vec(pnr);
    theta = 0.2;
    initial_dims = [];
    mappedX = fast_tsne(X,2,initial_dims,perplexity,theta);
    
    %% Save mapped data
    save([outdir sprintf('MappedHumanGenesAverage2Dperp%d',perplexity)],'X','mappedX','coords',...
        'initial_dims','perplexity','theta','selvec','color_RGB','structure_id','brain_id');
    
    %% Visualize mapped data based on t-SNE coordinates
    minx = min(mappedX);
    maxx = max(mappedX);
    maxval = max([abs(minx) abs(maxx)]);
    mappedab = mappedX*127/maxval;
    tC = makecform('lab2srgb');
    mappedRGB = applycform([75*ones(size(mappedab,1),1) mappedab],tC);
    
    %% Visualize mapped data using region colors
    nsamples = size(X,1);
    
    %
    figure(2)
    clf
    hold on
    for snr = 1:nsamples
        c = color_RGB(snr,:);
        plot(mappedX(snr,1),mappedX(snr,2),'.','Color',c);
    end
    
    saveas(2,[outdir sprintf('MappedHumanGenesGroupAverageRegions2Dperp%d',perplexity)]);
    
    %% Visualize mapped data using brain id colors
    nsamples = size(X,1);
    
    %
    figure(3)
    clf
    hold on
    cm = hsv(nbrains);
    for bnr = 1:nbrains
        c = cm(bnr,:);
        plot(mappedX(brain_id==bnr,1),mappedX(brain_id==bnr,2),'.','Color',c);
    end
    
    saveas(3,[outdir sprintf('MappedHumanGenesGroupAverageBrainID2Dperp%d',perplexity)]);
end