sc_umap.m

function s = sc_umap(X, ndim, donorm, dolog1p)
%UMAP embedding of cells
% s=sc_umap(X,3);

%see also: SC_TSNT, SC_PHATE
% s_phate=run.PHATE(X,3,true);
% s_umap=run.UMAP(X,3);

if nargin < 4, dolog1p = true; end
if nargin < 3, donorm = true; end
if nargin < 2, ndim = 3; end
% if ~issparse(X), X=sparse(X); end

if donorm
    X = sc_norm(X, 'type', 'libsize');
    disp('Library-size normalization...done.')
end
if dolog1p
    X = log1p(X);
    disp('log1p transformation...done.')
end
s = run.ml_UMAP(X, ndim);
end