sc_grnview.m

function sc_grnview(A, nodenames, figname, parentfig)
if nargin < 4, parentfig = []; end
if nargin < 3, figname = ''; end
%GRN network viewer
if isa(A, 'digraph') || isa(A, 'graph')
    G = A;
else
    if nargin < 2
        nodenames = string((1:size(A, 1))');
    end
    G = pkg.i_makegraph(A, nodenames);
end
if nargin < 3
    figname = sprintf('nodes (n=%d, red=TF); edges (blue=positive, red=negative)', ...
        G.numnodes);
end
gui.i_singlegraph(G, figname, parentfig);
end

%{
if nargin<3, cutoff=0.75; end
if nargin<2, g=[]; end
if isa(A,'digraph')||isa(A,'graph')
    g=string(A.Nodes.Name);
    A=adjacency(A,'weighted');
end
n=size(A,1);
if n>200, error('Smaller network is expected'); end
if isempty(g), g=string(1:n); end

% Add the UI components
hs = addcomponents;
[G,p]=drawnetwork(A,g,cutoff);
% Make figure visible after adding components
hs.fig.Visible = 'on';

function hs = addcomponents
% Add components, save handles in a struct
hs.fig = figure('Visible','off',...
    'Tag','fig',...
    'SizeChangedFcn',@resizeui, 'DockControls', 'off');

hs.btn = uicontrol(hs.fig,'String',...
    'Layout',...
    'Callback',@ChangeLayout,...
    'Tag','button');

hs.btn2 = uicontrol(hs.fig,'String',...
    'Weight',...
    'Callback',@ChangeWeight,...
    'Tag','button');

hs.btn3 = uicontrol(hs.fig,'String',...
    'Cutoff',...
    'Callback',@ChangeCutoff,...
    'Tag','button');

hs.btn4 = uicontrol(hs.fig,'String',...
    'Directed',...
    'Callback',@ChangeDirected,...
    'Tag','button');
hs.btn5 = uicontrol(hs.fig,'String',...
    'Font Size',...
    'Callback',@ChangeFontSize,...
    'Tag','button');
hs.btn6 = uicontrol(hs.fig,'String',...
    'Save Adj',...
    'Callback',@SaveAdj,...
    'Tag','button');

hs.ax = axes('Parent',hs.fig,...
    'Units','pixels',...
    'Tag','ax');
end

function ChangeLayout(hObject,event)
%plot(hs.ax,theta,y);
a=["layered","subspace","force","circle","force3","subspace3"];
i=randi(length(a));
p.layout(a(i));
if i>4
    view(3);
else
    view(2);
end
end

function ChangeWeight(hObject,event)
if length(unique(p.LineWidth))>1
    p.LineWidth = p.LineWidth./p.LineWidth;
else
    a=3:10;
    b=a(randi(length(a),1));
    G.Edges.LWidths = abs(b*G.Edges.Weight/max(G.Edges.Weight));
    p.LineWidth = G.Edges.LWidths;
end
end

function ChangeCutoff(hObject,event)
list = {'0.00 (show all edges)',...
    '0.30','0.35','0.40','0.45',...
    '0.50','0.55','0.60',...
    '0.65','0.70','0.75','0.80','0.85',...
    '0.90','0.95 (show 5% of edges)'};
[indx,tf] = listdlg('ListString',list,...
    'SelectionMode','single','ListSize', [220, 300]);
if tf
    if indx==1
        cutoff=0;
    elseif indx==length(list)
        cutoff=0.95;
    else
        cutoff=str2double(list(indx));
    end
    x=p.XData; y=p.YData; z=p.ZData;
    if isa(G,'idgraph')
        [G,p]=drawnetwork(A,g,cutoff);
    else
        [G,p]=drawnetwork(0.5*(A+A.'),g,cutoff);
    end
    p.XData=x; p.YData=y; p.ZData=z;
end
end

function ChangeDirected(hObject,event)
x=p.XData; y=p.YData; z=p.ZData;
if isa(G,'graph')
    [G,p]=drawnetwork(A,g,cutoff);
else
    [G,p]=drawnetwork(0.5*(A+A.'),g,cutoff);
end
p.XData=x; p.YData=y; p.ZData=z;
end

function ChangeFontSize(hObject,event)
if p.NodeFontSize>=20
    p.NodeFontSize=7;
else
    p.NodeFontSize=p.NodeFontSize+1;
end
end

function SaveAdj(hObject,event)
labels = {'Save adjacency matrix A to variable named:',...
    'Save graph G to variable named:',...
    'Save genelist g to variable named:'};
vars = {'A','G','g'}; values = {A,G,g};
msgfig=export2wsdlg(labels,vars,values);
uiwait(msgfig);
end

function resizeui(hObject,event)
% Get figure width and height
figwidth = hs.fig.Position(3);
figheight = hs.fig.Position(4);

% Set button position
bheight = 30;
bwidth = 70;
bbottomedge = figheight - bheight - 50;
bleftedge = 10;
hs.btn.Position = [bleftedge bbottomedge bwidth bheight];
hs.btn2.Position = [bleftedge bbottomedge-40 bwidth bheight];
hs.btn3.Position = [bleftedge bbottomedge-80 bwidth bheight];
hs.btn4.Position = [bleftedge bbottomedge-120 bwidth bheight];
hs.btn5.Position = [bleftedge bbottomedge-160 bwidth bheight];
hs.btn6.Position = [bleftedge bbottomedge-200 bwidth bheight];

% Set axes position
axheight = .85*figheight;
axbottomedge = max(0,figheight - axheight - 30);
axleftedge = bleftedge + bwidth + 10;
axwidth = max(0,figwidth - axleftedge - 30);
hs.ax.Position = [axleftedge axbottomedge axwidth axheight];
end

function [G,p]=drawnetwork(A,g,cutoff)
B=e_transf(A,cutoff);
if issymmetric(B)
    G=graph(B,g,'omitselfloops');
else
    G=digraph(B,g,'omitselfloops');
end
p=plot(hs.ax,G);
layout(p,'force');
if isa(G,'digraph')
    G.Nodes.NodeColors = outdegree(G)-indegree(G);
else
    G.Nodes.NodeColors = degree(G);
end
p.NodeCData = G.Nodes.NodeColors;
n=size(G.Edges,1);
cc=repmat([0 0.4470 0.7410],n,1);
cc(G.Edges.Weight<0,:)=repmat([0.8500, 0.3250, 0.0980],...
    sum(G.Edges.Weight<0),1);
p.EdgeColor=cc;
p.NodeFontSize=2*p.NodeFontSize;
%view(3)
title('Single-cell Gene Regulatory Netowrk');
end
end


function A=e_transf(A,q)
% A - adjacency matrix
if nargin<2, q=0.95; end
dim=size(A);
if numel(dim)==2
a=max(abs(A(:)));
if a>0
    A=A./a;
    A=A.*(abs(A)>quantile(abs(A(:)),q));
end
elseif numel(dim)==3
for k=1:dim(3)
    A(:,:,k)=e_transf(A(:,:,k),q);
end
end
end
%}