parse_in_vitro.m
b83a89f7c134master

parse_in_vitro.m
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			% PARSE_IN_VITRO produces the plots necessary to the in vitro review
			%
			% Blanchoud Group, UNIFR
			% Simon Blanchoud
			% 15/12/2021
			function parse_in_vitro

			% Location of the reference files
			pub_file = '/home/blanchou/Documents/Manuscripts/MARISTEM_review/dataset/curated_publications_v3.csv'

			fid = fopen(pub_file);
			data = textscan(fid, '%d,%s,%s,%q', 'HeaderLines', 1, 'Delimiter', ',');
			fclose(fid);

			year = data{1};
			taxa = data{2};
			order = data{3};
			phyla = unique(taxa);
			classes = unique(order);
			groups = NaN(numel(year), numel(phyla));
			subgroups = NaN(numel(year), numel(classes));

			count = 1;
			l = {};
			for i=1:length(phyla)
			iscurr = ismember(taxa, phyla{i});
			groups(iscurr, i) = year(iscurr);


			currclasses = unique(order(iscurr));
			for j=1:length(currclasses)
			iscurr = ismember(order, currclasses{j});
			subgroups(iscurr, count) = year(iscurr);
			l{count} = currclasses{j};
			count = count+1;
			end
			end

			x = [1968:3:2022].';
			y = histc(groups, x);
			y2 = histc(subgroups, x);

			figure;bar(x,y, 'stacked')
			figure;bar(x,y2, 'stacked')
			legend(l)

			keyboard

			return
			end