70 lines
2.5 KiB
Matlab
70 lines
2.5 KiB
Matlab
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close all
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%load mean_coverage_per_exon_per_pool.mat <-- doesn't work from
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%/sting/matlab -- but this does
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imp = importdata('/humgen/gsa-hphome1/projects/FHS/results/production_averageDoCByExonAndGene.txt');
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data = imp.data;
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textdata = imp.textdata;
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pilot_pos = ismember(textdata(:,2),'CEPH3')+ismember(textdata(:,2),'CEPH2')+ismember(textdata(:,2),'CEPH1');
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pilot_data = data( find(pilot_pos == 1), : );
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prod_data = data( find(pilot_pos == 0) , :);
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pilot_text = textdata( find ( pilot_pos == 1) , : );
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prod_text = textdata( find ( pilot_pos == 0 ), : );
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lim = length(data);
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% get unique names
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gnames = [textdata(1,3)];
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prevn = 'hello doofus';
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for ii = 2 : lim/23 % first 1/23 of the file contains all the gene names (rest are repeats)
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n = textdata{ii,3};
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if ( length(prevn) == length(n) && prevn(1)==n(1) && prevn(end)==n(end) )
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% quick test to check if gene is same as previous
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else
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if ( ~ ismember(gnames,n) )
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gnames = [gnames; textdata(ii,3)];
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% more exhaustive test to see if gene name is novel
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end
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prevn = n;
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end
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end
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% plot the groups
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num_genes = size(gnames) % yes we want to print this
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to_plot = 40;
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plotno = 0;
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filenamebaseprod = 'FHS_production_gene_cvg_boxplot_';
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filenamebasepilot = 'FHS_pilot_gene_cvg_boxplot_';
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for genes = 1 : to_plot : num_genes
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plotno = plotno + 1;
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pilot_positions = [];
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prod_positions = [];
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for g = genes:genes+to_plot
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%n = gnames{g,1}
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if ( g < length(gnames) )
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pilot_positions = [pilot_positions; find(ismember(pilot_text(:,3),gnames{g,1}) == 1)];
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prod_positions = [prod_positions; find(ismember(prod_text(:,3),gnames{g,1}) == 1 )];
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end
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end
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depths_prod = prod_data(prod_positions,2);
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depths_pilot = pilot_data(pilot_positions,2);
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grenes_prod = prod_text(prod_positions,3);
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grenes_pilot = pilot_text(pilot_positions,3);
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h = figure
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hp = subplot(1,1,1)
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boxplot(depths_prod,grenes_prod,'plotstyle','compact','orientation','vertical','datalim',[0,10000],'whisker',0,'symbol','r+'), title('Production')
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set(hp,'YLim',[-1000,11000])
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y = figure
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yp = subplot(1,1,1)
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boxplot(depths_pilot,grenes_pilot,'plotstyle','compact','orientation','vertical','datalim',[0,10000],'whisker',0,'symbol','r+'), title('Pilot')
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set(yp,'YLim',[-1000,11000])
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% -- uncomment these lines to save the files --
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%saveas(h,strcat(filenamebaseprod,num2str(plotno)),'psc2');
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%saveas(y,strcat(filenamebasepilot,num2str(plotno)),'psc2');
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end
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