tsne_on_human_genes_selection_sweep.m

%% Perform Barnes-Hut t-SNE on human gene data with a perplexity sweep
clear variables
close all

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

perplexities = 1:10;
nperp = length(perplexities);

for pnr = 1:nperp
    for bnr = 1:2
        %% Load data (currently for a single brain)
        id = ids{bnr};
        datadir = ['/home/mvandegiessen/data/tSNE_ABA/rawData_25Feb2014/normalized_microarray_donor' id '/'];
        expressionlevels = load([datadir 'MicroarrayExpression']);
        
        % Load gene selection
        indexdata = load([datadir 'probe2gene_index']);
        allgindices = 1:size(expressionlevels.MicroarrayExpression,1);
        selgenes = allgindices(indexdata.probe2gene_index>0);
        ngenes = length(selgenes);
        
        % Load gene coordinates
        coordsdata = load([datadir 'sample']);
        coords = [coordsdata.sample.mni_x,coordsdata.sample.mni_y,coordsdata.sample.mni_z];
        
        %% Perform t-SNE
        % Data subselection
        X = expressionlevels.MicroarrayExpression';
        X = X(:,selgenes);
        
        % Perform t-SNE
        perplexity = perplexities(pnr);
        theta = 0.7;
        initial_dims = min(1000,size(X,2));
        mappedX = fast_tsne(X,2,initial_dims,perplexity,theta);
        
        %% Save mapped data
        save(['MappedGenesSelection' id sprintf('_Perp%d',perplexities(pnr))],'X','mappedX','selgenes','coords',...
            'initial_dims','perplexity','theta');
        
        %% Visualize mapped data
        % Colorspace
        crange = max(coords)-min(coords);
        mincoords = min(coords);
        nsamples = size(X,1);
        
        %
        figure(1)
        clf
        hold on
        for snr = 1:nsamples
            c = (coords(snr,:)-mincoords)./crange;
            plot(mappedX(snr,1),mappedX(snr,2),'.','Color',c);
        end
        
        figure(2)
        clf
        hold on
        for snr = 1:nsamples
            c = coordsdata.sample.color_RGB(snr,:);
            plot(mappedX(snr,1),mappedX(snr,2),'.','Color',c);
        end
        saveas(2,['MappedGenesSelection' id sprintf('_Perp%d',perplexities(pnr)) '.png']);
        
        % saveas(1,'MappedGenesSelection');
    end
end