BeadSorting.m

function successmessage=BeadSorting(filepath,file_range)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% file:BeadSorting.m
% ***Description***:
% This function serves automatically search for Bead Peaks and sort them
% from the Cell peaks in Blood samples where Beads were also spiked.
% Currently this function is run from within SamplePeakDetection.m function
% when a flag indicated Beads were added to blood sample.
% Written By: Nilay Vora (nvora01@tufts.edu)
% Date Written: 01/13/2022
% Modifying Author:Nilay Vora
% Date Modified: 01/19/2022
% Latest Revision: Manually modified indexing due to error in lines 49-52,
% not sure if this is the right correction.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Function details
% Inputs:
%   filepath = Location of all main folder where all subfolders are
%   file_range = Which files do you want to analyze in a specific day
% Outputs:
%   successmessage = a string that indicates the completion of the code
%
% Usage SamplePeakDetection(filepath,file_range)
% Example:
% filepath = 'U:\Nilay\IVFC\Acquired Data\Blood Data\NV_092821_Blood_LNPs';
% file_range= [1:3];
% 
% output=SamplePeakDetection(filepath,file_range)
%% Initialization
clc
%% Find Folders
mainFolder=filepath;
cd(mainFolder)


dirinfo = dir();
dirinfo(~[dirinfo.isdir]) = [];  %remove non-directories

dirinfo(ismember( {dirinfo.name}, {'.', '..'})) = [];  %remove . and ..
[~,c]=natsortfiles({dirinfo.name});
subdirinfo = cell(length(dirinfo));

for K = 1 : length(dirinfo)
    thisdir = dirinfo(c(K)).name;
    subdirinfo{K} = dir(fullfile(thisdir, '*RFLR.mat'));
end

subdirinfo =  subdirinfo(~cellfun('isempty',subdirinfo));

if file_range(1)~=1
    file_range=file_range-(file_range(1)-1);
end
%% Main Loop: Split the Cells from Beads
for i=file_range
    disp(['Evaluating File # ',num2str(i),' of ',num2str(size(subdirinfo,1))]);
    del=[]; % Matrix of bead peaks
    truepeaks=[]; % Matrix of cell peaks
    if~isempty(subdirinfo{i})
        cd(subdirinfo{i}(1).folder)
        load(subdirinfo{i}(1).name)
        pv1=peak_values;
        chunks=unique(peak_values(:,6));
        for j=min(chunks):max(chunks)
            disp(['Chunk # ',num2str(j),' of ',num2str(max(chunks))]);
            a=pv1(:,6)==j;
            loc=pv1(a,7);
            load([subdirinfo{i}(1).name(1:end-8),'NoScatAll.mat'],'peak_values')
            pv2=peak_values;
            a2=find(pv2(:,6)==j);
            loc2=pv2(a2,7);
            wid2=pv2(a2,9);
            for k=1:length(loc2)
                l2=loc2(k);
                match=find(loc>=l2-wid2(k).*1.5 & loc<=l2+wid2(k).*1.5,1);
                if ~isempty(match)
                    del=[del;pv2(a2(k),:)]; %#ok<AGROW> 
                else
                    truepeaks=[truepeaks;pv2(a2(k),:)]; %#ok<AGROW> 
                end
            end
        end
        peak_values=truepeaks;
        save([subdirinfo{i}(1).name(1:end-8),'NoScatCell.mat'],'peak_values')
        peak_values=del;
        save([subdirinfo{i}(1).name(1:end-8),'NoScatBeads.mat'],'peak_values')
    end 
end

%% Save all sorted files
pv1=[];
pv2=[];
for i=file_range
    disp(['Evaluating File # ',num2str(i),' of ',num2str(size(subdirinfo,1))]);
    if~isempty(subdirinfo{i}(1))
        cd(subdirinfo{i}(1).folder)
        load([subdirinfo{i}(1).name(1:end-8),'NoScatBeads.mat'],'peak_values')
        pv1=[pv1;peak_values]; %#ok<AGROW> 
        load([subdirinfo{i}(1).name(1:end-8),'NoScatCell.mat'],'peak_values')
        pv2=[pv2;peak_values]; %#ok<AGROW> 
    end
end
cd(mainFolder)
 peak_values=pv1;
 save([subdirinfo{i}(1).name(4:end-8),'NoScatBeads.mat'],'peak_values')
 peak_values=pv2;
 save([subdirinfo{i}(1).name(4:end-8),'NoScatCell.mat'],'peak_values')
successmessage='Completed Seperating Bead Peaks';