stitch_export.m

function stitch_export(path, DataSet, G, XY, gene_names)
% Usage: stitch_export(path, DataSet, G, XY, gene_names)
%
% Export attributes of the STITCH graph (e.g. for import into ScanPy):
% 
% INPUTS:
% path              Name of directory to write files (string).
% DataSet           STITCH Data structure 
% G                 STITCH Graph object
% XY                XY coordinates imported from Gephi
% gene_names        Object containing gene names (cell array of strings)
%
% OUTPUT FILES:
%  genes.txt        Gene names
%  counts.csv       Genes x cells counts matrix
%  annot.txt        Annotation flags for each cell (DataSet.celldata)
%  timepoints.txt   Timepoint/sample flags for each cell (DataSet.name)
%  edges.csv        Edge table for G
%  coordinates.txt  XY coordinates for each node of graph object G
%
%% SETTINGS:
%path = 'export';

%% CODE:

% check that export directory exists
if ~exist(path, 'dir')
    mkdir(path);
end

% export gene names
disp('Exporting gene names...')
writetable(cell2table(gene_names), [path '/' 'genes.txt'],'WriteVariableNames',0)

% get original indices of cells in G
tmp_cell_ind = str2num(cell2mat(G.Nodes.Name));

% export counts matrix
disp('Exporting counts matrix...')
tmp_X = [];
nTimePoints = length(DataSet);
for j = nTimePoints:-1:1
    tmp_X = [tmp_X DataSet(j).X]; 
end
tmp_X = tmp_X(:,tmp_cell_ind);
dlmwrite([path '/' 'counts.csv'], full(tmp_X)',',')
clear tmp_X

% export flags for each annotation column in DataSet.celldata
disp('Exporting annotations...')
nAnnots = length(DataSet(1).celldata.Properties.VariableNames);
for k = 1:nAnnots
    tmp_IDs = [];
    for j = nTimePoints:-1:1
        tmp_IDs = [tmp_IDs; DataSet(j).celldata(:,k)]; 
    end
    tmp_IDs = tmp_IDs(tmp_cell_ind,:);
    writetable(tmp_IDs, [path '/' DataSet(j).celldata.Properties.VariableNames{k} '.txt'],'WriteVariableNames',0);
end

% export timepoint/sample flags 
disp('Exporting timepoints...')
tmp_timepoint_names = [];
tmp_timepoints = [];
for j = nTimePoints:-1:1
    tmp_timepoint_names = [tmp_timepoint_names; repmat(DataSet(j).name,size(DataSet(j).X,2),1)]; 
    tmp_timepoints = [tmp_timepoints; repmat(DataSet(j).ind,size(DataSet(j).X,2),1)];
end
tmp_timepoint_names = tmp_timepoint_names(tmp_cell_ind);
tmp_timepoints = tmp_timepoints(tmp_cell_ind);
writetable(table(tmp_timepoint_names), [path '/' 'timepoint_names.txt'],'WriteVariableNames',0);
writetable(table(tmp_timepoints), [path '/' 'timepoints.txt'],'WriteVariableNames',0);

% edge table
disp('Exporting edge list...')
dlmwrite([path '/' 'edges.csv'], get_indexed_edge_list(G), ';');

% export XY coordinates
disp('Exporting XY coordinates...')
tmp_ind = 0:length(XY)-1;
tmp_XY = [tmp_ind' XY(:,1) -1*XY(:,2)]; % invert Y axis to match SPRING layout
dlmwrite([path '/' 'coordinates.txt'],tmp_XY,',')
disp('Done!')