.

+gui/callback_scTenifoldCko.m

@@ -128,35 +128,39 @@ function callback_scTenifoldCko(src, ~)
 
 switch Cko_approach
     case 'Block Ligand-Receptor'
-        [indx2, tf] = listdlg('PromptString', {'Select a ligand-receptor pair (two genes)'}, ...
-            'SelectionMode', 'multiple', 'ListString', gsorted, 'ListSize', [220, 300]);
-        if tf == 1
-            if numel(indx2)==2
-                [~, idx] = ismember(gsorted(indx2), sce.g);
-            else
-                return;
-            end
+
+        [idx2] = gui.i_selmultidlg(gsorted, [], FigureHandle);
+        if isempty(idx2), return; end
+        if numel(idx2)==2
+            [~, idx] = ismember(gsorted(idx2), sce.g);
         else
             return;
         end
         targetg = sce.g(idx);
 
+
         targetpath = ...
-        [sprintf('%s (%s) -> %s (%s)', celltype1, targetg(1), celltype2, targetg(2));...
+        string([sprintf('%s (%s) -> %s (%s)', celltype1, targetg(1), celltype2, targetg(2));...
         sprintf('%s (%s) -> %s (%s)', celltype1, targetg(2), celltype2, targetg(1));...
         sprintf('%s (%s) <- %s (%s)', celltype1, targetg(1), celltype2, targetg(2));...
-        sprintf('%s (%s) <- %s (%s)', celltype1, targetg(2), celltype2, targetg(1))];
-
+        sprintf('%s (%s) <- %s (%s)', celltype1, targetg(2), celltype2, targetg(1))]);
+        [width] = min([max(strlength(targetpath))*6, 500]);
         [indx2, tf] = listdlg('PromptString', {'Select path(s) to block:'}, ...
-            'SelectionMode', 'multiple', 'ListString', targetpath, 'ListSize', [220, 300]);
-
+            'SelectionMode', 'multiple', 'ListString', targetpath, 'ListSize', [width, 300]);
         if tf == 1
             targetpath = targetpath(indx2);
         else
             return;
         end
-        [Tcell] = run.py_scTenifoldCko(sce, celltype1, celltype2, targetg, ...
-            targetpath, wkdir, true, prepare_input_only);
+        celltype1
+        celltype2
+        targetg
+        targetpath
+
+
+        return;
+        %[Tcell] = run.py_scTenifoldCko_path(sce, celltype1, celltype2, targetg, ...
+        %    targetpath, wkdir, true, prepare_input_only);
 
 
     case 'Complete Gene Knockout'
@@ -185,106 +189,104 @@ function callback_scTenifoldCko(src, ~)
         [Tcell] = run.py_scTenifoldCko_type(sce, celltype1, celltype2, targetg, ...
             targettype, wkdir, true, prepare_input_only);
     otherwise
-
+        errordlg('Invalid option.','');
+        return;
 end
 
 
-
-
-
-if ~isempty(Tcell)
-    [T1] = Tcell{1};
-    [T2] = Tcell{2};
-    if ~isempty(T1)
-        a = sprintf('%s -> %s', celltype1, celltype2);
-        T1 = addvars(T1, repelem(a, height(T1), 1), 'Before', 1);
-        T1.Properties.VariableNames{'Var1'} = 'direction';
-    end
-    if ~isempty(T2)
-        a = sprintf('%s -> %s', celltype2, celltype1);
-        T2 = addvars(T2, repelem(a, height(T2), 1), 'Before', 1);
-        T2.Properties.VariableNames{'Var1'} = 'direction';
+    if ~isempty(Tcell)
+        [T1] = Tcell{1};
+        [T2] = Tcell{2};
+        if ~isempty(T1)
+            a = sprintf('%s -> %s', celltype1, celltype2);
+            T1 = addvars(T1, repelem(a, height(T1), 1), 'Before', 1);
+            T1.Properties.VariableNames{'Var1'} = 'direction';
+        end
+        if ~isempty(T2)
+            a = sprintf('%s -> %s', celltype2, celltype1);
+            T2 = addvars(T2, repelem(a, height(T2), 1), 'Before', 1);
+            T2.Properties.VariableNames{'Var1'} = 'direction';
+        end
+        T = [T1; T2];
     end
-    T = [T1; T2];
-end
-
-if ~isempty(T)
-    mfolder = fileparts(mfilename('fullpath'));
-    load(fullfile(mfolder, '..', 'resources', 'Ligand_Receptor', ...
-         'Ligand_Receptor_more.mat'), 'ligand','receptor');
-    A = [string(T.ligand) string(T.receptor)];
-    B = [ligand receptor];
-    [knownpair]= ismember(A, B, 'rows');
-    assert(length(knownpair)==height(T));
-
-    T=[T, table(knownpair)];
-    % T(:,[4 5 6 7 11])=[];
 
-    outfile = fullfile(wkdir,"outfile.csv");
-    if isfile(outfile)
-        answerx = questdlg('Overwrite outfile.csv? Select No to save in a temporary file.');
-    else
-        answerx = 'Yes';
-    end
-    if isempty(wkdir) || ~isfolder(wkdir) || ~strcmp(answerx, 'Yes')
-        [a, b] = pkg.i_tempdirfile("sctendifoldcko");
-        writetable(T, b);
+    if ~isempty(T)
+        mfolder = fileparts(mfilename('fullpath'));
+        load(fullfile(mfolder, '..', 'resources', 'Ligand_Receptor', ...
+             'Ligand_Receptor_more.mat'), 'ligand','receptor');
+        A = [string(T.ligand) string(T.receptor)];
+        B = [ligand receptor];
+        [knownpair]= ismember(A, B, 'rows');
+        assert(length(knownpair)==height(T));
 
-        answer = questdlg(sprintf('Result has been saved in %s', b), ...
-            '', 'Export result...', 'Locate result file...', 'Export result...');
-        switch answer
-            case 'Locate result file...'
-                winopen(a);
-                pause(2)
-                if strcmp(questdlg('Export result to other format?'), 'Yes')
+        T=[T, table(knownpair)];
+        % T(:,[4 5 6 7 11])=[];
+
+        outfile = fullfile(wkdir,"outfile.csv");
+        if isfile(outfile)
+            answerx = questdlg('Overwrite outfile.csv? Select No to save in a temporary file.');
+        else
+            answerx = 'Yes';
+        end
+        if isempty(wkdir) || ~isfolder(wkdir) || ~strcmp(answerx, 'Yes')
+            [a, b] = pkg.i_tempdirfile("sctendifoldcko");
+            writetable(T, b);
+
+            answer = questdlg(sprintf('Result has been saved in %s', b), ...
+                '', 'Export result...', 'Locate result file...', 'Export result...');
+            switch answer
+                case 'Locate result file...'
+                    winopen(a);
+                    pause(2)
+                    if strcmp(questdlg('Export result to other format?'), 'Yes')
+                        gui.i_exporttable(T, false, 'Ttenifldcko', 'TenifldCkoTable');
+                    end
+                case 'Export result...'
                     gui.i_exporttable(T, false, 'Ttenifldcko', 'TenifldCkoTable');
-                end
-            case 'Export result...'
-                gui.i_exporttable(T, false, 'Ttenifldcko', 'TenifldCkoTable');
-            otherwise
-                winopen(a);
+                otherwise
+                    winopen(a);
+            end
+        else
+            writetable(T, outfile);
+            waitfor(helpdlg(sprintf('Result has been saved in %s', outfile), ''));
         end
     else
-        writetable(T, outfile);
-        waitfor(helpdlg(sprintf('Result has been saved in %s', outfile), ''));
-    end
-else
-    if ~prepare_input_only
-        helpdlg('No ligand-receptor pairs are identified.', '');
-    else
-        if strcmp(questdlg('Input files are prepared successfully. Open working folder?',''), 'Yes')
-            winopen(wkdir);
+        if ~prepare_input_only
+            helpdlg('No ligand-receptor pairs are identified.', '');
+        else
+            if strcmp(questdlg('Input files are prepared successfully. Open working folder?',''), 'Yes')
+                winopen(wkdir);
+            end
         end
     end
-end
-
-fn=fullfile(wkdir, 'merged_embeds.h5');
-
-eb = h5read(fn,'/data')';
-
-n = height(eb);
-sl = n / 4;
-
-% Split the eb into four equal-length sub-ebs
-a = eb(1:sl,:);
-b = eb(sl+1:2*sl,:);
-c = eb(2*sl+1:3*sl,:);
-d = eb(3*sl+1:4*sl,:);
-
-%dx = abs(pdist2(a,b)-pdist2(c,d));
-%[x,y]=pkg.i_maxij(dx, 1050);
-%[sce.g(x) sce.g(y)]
-%dx1 = pdist2(a,c);
-%dx1 = pdist2(b,d);
-%[x,y]=maxij(dx1, 50);
-%[sce.g(x) sce.g(y)]
-
-[T] = ten.i_dr(a, c, sce.g, true);
-outfile = sprintf('outfile_%s_expression_changes.csv',celltype1);
-writetable(T, outfile);
-
-[T] = ten.i_dr(b, d, sce.g, true);
-outfile = sprintf('outfile_%s_expression_changes.csv',celltype1);
-writetable(T, outfile);
+
+    fn=fullfile(wkdir, 'merged_embeds.h5');
+
+    eb = h5read(fn,'/data')';
+
+    n = height(eb);
+    sl = n / 4;
+
+    % Split the eb into four equal-length sub-ebs
+    a = eb(1:sl,:);
+    b = eb(sl+1:2*sl,:);
+    c = eb(2*sl+1:3*sl,:);
+    d = eb(3*sl+1:4*sl,:);
+
+    %dx = abs(pdist2(a,b)-pdist2(c,d));
+    %[x,y]=pkg.i_maxij(dx, 1050);
+    %[sce.g(x) sce.g(y)]
+    %dx1 = pdist2(a,c);
+    %dx1 = pdist2(b,d);
+    %[x,y]=maxij(dx1, 50);
+    %[sce.g(x) sce.g(y)]
+
+    [T] = ten.i_dr(a, c, sce.g, true);
+    outfile = sprintf('outfile_%s_expression_changes.csv',celltype1);
+    writetable(T, outfile);
+
+    [T] = ten.i_dr(b, d, sce.g, true);
+    outfile = sprintf('outfile_%s_expression_changes.csv',celltype1);
+    writetable(T, outfile);
 
 end

+gui/i_measuretext.m

@@ -0,0 +1,17 @@
+function [width, height] = i_measuretext(txt, textOpts, axis)
+    if nargin < 3
+       axis = gca(); 
+    end
+    if nargin < 2
+        textOpts = struct();
+        textOpts.HorizontalAlignment = 'center';
+        textOpts.VerticalAlignment = 'middle';
+        textOpts.FontSize = 20;
+        textOpts.FontWeight = 'normal';
+    end
+    hTest = text(axis, 0, 0, txt, textOpts);
+    textExt = get(hTest, 'Extent');
+    delete(hTest);
+    height = textExt(4)/3;    %Height
+    width = textExt(3)/3;     %Width
+end

+gui/i_singlegraph.m

@@ -455,8 +455,8 @@ function stopDragFcn(~, ~)
         h = graph(s, t);
 end
 
- function [width, height] = measureText(txt, textOpts, axis)
-    if(nargin < 3)
+function [width, height] = measureText(txt, textOpts, axis)
+    if nargin < 3
        axis = gca(); 
     end
     if nargin < 2