call_mcImpute.m

function [Xrec,normalizedXrec,geneGilteredXrec, gene_names] = call_mcImpute(data,varargin)
% calling fucntion for mcImpute

% MANDATORY ARGUMENT-> data: scRNA seq data matrix (cell x gene)
% 
%OPTIONAL ARGUMENT-> dataname: string having dataname, to save library size
%                    of data with unique name
%OPTIONAL ARGUMENT-> gene_names, gene_ids
%OPTIONAL ARGUMENT-> pro_dir: path to directory where processed matrix
%                    should be saved, if not specified a new directory would be created in
%                    current folder and processed data would be saved their

if(nargin<1)
    error('Expression matrix not provided!')
end
%% variables initialization
dataname='NEWDATA'; gene_names=[]; gene_ids=[]; pro_dir='./processed_data/';

if ~isempty(varargin)
    for j = 1:length(varargin)
       
        if strcmp(varargin{j}, 'dataname')
            dataname = varargin{j+1};
        end
    
        if strcmp(varargin{j}, 'gene_names')
            gene_names = varargin{j+1};
        end
        
        if strcmp(varargin{j}, 'gene_ids')
            gene_ids = varargin{j+1};
        end
        
        if strcmp(varargin{j}, 'pro_dir')
            pro_dir = varargin{j+1};
        end
        
    end
end

%{ 
elseif (nargin<2)
    dataname='NEWDATA'; gene_names=[]; gene_ids=[]; pro=1;
    warning('Dataname not provided..library size saved with prefix NEWDATA..')
elseif(nargin<3)
    gene_names=[]; gene_ids=[]; pro=1;
elseif(nargin<4)
    gene_ids=1:length(gene_names); pro=1;
else
    pro=1;
end
%}



if ~exist('Temp','dir'), mkdir Temp; end
if ~exist(pro_dir,'dir'), mkdir processedData; pro_dir='processedData/'; end


%% Process data
pro=1;
if (pro)
disp('Processing data.....')
[processed_data,gene_names] = process(data,dataname,gene_names, gene_ids); %processed_data=data
save([pro_dir '' dataname '_processed.mat'],'processed_data')
end

%% Run mcimpute
IDX = find(processed_data);
M = opRestriction(numel(processed_data),IDX);
y = M(processed_data(:),1);
 
[Xrec] = IST_MC(y,M,size(processed_data),0); %mask changed and lansvd changed, with NN constraint
%Xrec = IST_eMC(y,M,size(processed_data),11); 

normalizedXrec=2.^(Xrec)-1;
geneGilteredXrec=round(reverse_processing(dataname, Xrec));



end