sc_cluster_x.m

function [c] = sc_cluster_x(X, k, varargin)
%sc_cluster_x - cluster cells using UMI matrix X
%
%see also: sc_cluster_s

p = inputParser;
defaultType = 'sc3';
validTypes = {'sc3', 'simlr', 'soptsc', 'sinnlrr', 'specter'};
checkType = @(x) any(validatestring(x, validTypes));

checkK = @(x) (x > 0) && isnumeric(x) && isscalar(x);

addRequired(p, 'X', @isnumeric);
addRequired(p, 'k', checkK);
addOptional(p, 'type', defaultType, checkType);
addOptional(p, 'usehvgs', true);

parse(p, X, k, varargin{:})

if p.Results.usehvgs
    disp('Using 2000 HVGs.')
    [~, X] = sc_splinefit(X, [], true, false);
    X = X(1:min([size(X, 1), 2000]), :);
end

switch p.Results.type
    case 'simlr'
        % disp('To specify k, use RUN_SIMLR(X,k).');
        [c] = run.ml_SIMLR(X, k, true);
    case 'soptsc'
        % Symmetric NMF for cell clustering
        % https://www.biorxiv.org/content/biorxiv/early/2019/01/01/168922.full.pdf
        %disp('To specify k, use RUN_SOPTSC(X,''k'',k).');
        [c] = run.ml_SoptSC(X, 'k', k, 'donorm', true);
    case 'sc3'
        %disp('To specify k, use SC_SC3(X,k).');
        [c] = run.ml_SC3(X, k);
    case 'sinnlrr'
        % disp('To specify k, use RUN_SINNLRR(X,k).');
        [c] = run.ml_SinNLRR(X, k);
    case 'specter'
        [c] = run.ml_Specter(X, k);
    case 'alona'
        warning('In development.');
        % [C]=sc_alona(X);
end
end