sc_potency.m

function [r] = sc_potency(X, genelist, speciesid)
%Estimate differentiation potency of cells
%without the need to assume prior biological knowledge
%such as marker expression or timepoint.
% CCAT (Correlation of Connectome And Transcriptome)
%https://github.com/aet21/SCENT
%
%see also: run.cytotrace

if nargin < 3, speciesid = 1; end
    if ~ ismember(speciesid, [1 2])
        error('Invalid SPECIESID');
    end
 
    pw1 = fileparts(mfilename('fullpath'));
    % pth=fullfile(pw1,'resources/STRING');
    dbfile1 = fullfile(pw1, 'resources', 'STRING', 'stringdb_human.mat');
    dbfile2 = fullfile(pw1, 'resources', 'STRING', 'stringdb_mouse.mat');
    if ~ exist(dbfile1, 'file')
        %disp('Downloading ...... stringdb_human.mat')
        url = 'https://github.com/jamesjcai/jamesjcai.github.io/raw/master/data/stringdb_human.mat';
        % outfilename =
        websave(dbfile1, url);
    end
    if ~ exist(dbfile2, 'file')
        %disp('Downloading ...... stringdb_mouse.mat')
        url = 'https://github.com/jamesjcai/jamesjcai.github.io/raw/master/data/stringdb_mouse.mat';
        %outfilename =
        websave(dbfile2, url);
    end
 
    genelist = upper(genelist);
    if speciesid == 1
        ppinetfile = dbfile1; % 'Z:\Cailab\CCC_utilities\STRING\stringdb_human.mat';
        disp('Using resources/stringdb_human.mat')
    else
        ppinetfile = dbfile2; % 'Z:\Cailab\CCC_utilities\STRING\stringdb_mouse.mat';
        disp('Using resources/stringdb_mouse.mat')
    end
    load(ppinetfile, 'G');
    G.Edges.Weight = double(G.Edges.Weight > 0);
    GNodes = upper(string(table2array(G.Nodes)));
    Gdegree = G.degree;
    X = log2(X + 1.1);
 
    [~, i, j] = intersect(genelist, GNodes);
    if isempty(i)
        error(sprintf('No gene is found in STRING PPI data base.\nCheck gene names.'));
    end
    d = Gdegree(j);
    X = X(i, :);
    r = corr(X, d); % Correlation of Connectome And Transcriptome
 
end