.

+gui/callback_SelectCellsByQC.m

@@ -10,6 +10,9 @@
 sce = guidata(FigureHandle);
 % 'SC_QCFILTER (QC Preserves Lowly-expressed Cells/Genes)',...
 
+oldcn = sce.NumCells;
+oldgn = sce.NumGenes;
+
 listitems = {'SC_QCFILTER (Basic QC for Cells/Genes)', ...
         'SC_QCFILTER (Enabling Whitelist Genes)', ...
         '------------------------------------------------', ...
@@ -445,6 +448,30 @@
             return;
         end
     end
+
+    newcn = sce.NumCells;
+    newgn = sce.NumGenes;
+    if newgn==0
+        helpdlg("All genes are removed. Opertaion is cancelled.",'');
+        requirerefresh = false;
+        return;
+    end
+    if newcn==0
+        helpdlg("All cells are removed. Opertaion is cancelled.",'');
+        requirerefresh = false;
+        return;
+    end
+    if oldcn-newcn==0 && oldgn-newgn==0
+        helpdlg("No cells and genes are removed.",'');
+        requirerefresh = false;
+        return;
+    end
+    answer = questdlg(sprintf('%d cells will be removed; %d genes will be removed.', ...
+            oldcn-newcn, oldgn-newgn),'','Accept Changes', 'Cancel Changes', 'Accept Changes');
+    if ~strcmp(answer, 'Accept Changes')
+        requirerefresh = false;
+        return;
+    end
     guidata(FigureHandle, sce);
 end
 

+gui/callback_scTenifoldCko.m

@@ -116,12 +116,6 @@ function callback_scTenifoldCko(src, ~)
 gsorted = natsort(sce.g);
 if isempty(gsorted), return; end
 
-
-
-
-
-
-
 Cko_approach = questdlg('Select CKO approach:','','Block Ligand-Receptor','Complete Gene Knockout','Block Ligand-Receptor');
 if ~ismember(Cko_approach, {'Block Ligand-Receptor','Complete Gene Knockout'}), return; end
 
@@ -142,27 +136,24 @@ function callback_scTenifoldCko(src, ~)
         targetpath = ...
         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));...
+        sprintf('%s (%s) <- %s (%s)', celltype1, targetg(1), celltype2, targetg(2))]);
         [width] = min([max(strlength(targetpath))*6, 500]);
-        [indx2, tf] = listdlg('PromptString', {'Select path(s) to block:'}, ...
+        [targetpathid, tf] = listdlg('PromptString', {'Select path(s) to block:'}, ...
             'SelectionMode', 'multiple', 'ListString', targetpath, 'ListSize', [width, 300]);
-        if tf == 1
-            targetpath = targetpath(indx2);
-        else
-            return;
-        end
-        celltype1
-        celltype2
-        targetg
-        targetpath
-
-
-        return;
-        %[Tcell] = run.py_scTenifoldCko_path(sce, celltype1, celltype2, targetg, ...
-        %    targetpath, wkdir, true, prepare_input_only);
+        if tf ~= 1, return; end
+
+        % assignin("base","sce",sce)
+        % assignin("base","celltype1",celltype1)
+        % assignin("base","celltype2",celltype2)
+        % assignin("base","targetg",targetg)
+        % assignin("base","targetpathid",targetpathid)
+        % prepare_input_only = true;
 
-
+        [Tcell] = run.py_scTenifoldCko_path(sce, celltype1, celltype2, targetg, ...
+            targetpathid, wkdir, true, prepare_input_only);
+
+        % return;
     case 'Complete Gene Knockout'
         [indx2, tf] = listdlg('PromptString', {'Select a KO gene'}, ...
             'SelectionMode', 'single', 'ListString', gsorted, 'ListSize', [220, 300]);
@@ -186,13 +177,12 @@ function callback_scTenifoldCko(src, ~)
         end
 
         T = [];
-        [Tcell] = run.py_scTenifoldCko_type(sce, celltype1, celltype2, targetg, ...
+        [Tcell] = run.py_scTenifoldCko_gene(sce, celltype1, celltype2, targetg, ...
             targettype, wkdir, true, prepare_input_only);
     otherwise
         errordlg('Invalid option.','');
         return;
 end
-
 
     if ~isempty(Tcell)
         [T1] = Tcell{1};
@@ -222,9 +212,9 @@ function callback_scTenifoldCko(src, ~)
         T=[T, table(knownpair)];
         % T(:,[4 5 6 7 11])=[];
 
-        outfile = fullfile(wkdir,"outfile.csv");
+        outfile = fullfile(wkdir,"outfile_interaction_changes.csv");
         if isfile(outfile)
-            answerx = questdlg('Overwrite outfile.csv? Select No to save in a temporary file.');
+            answerx = questdlg('Overwrite file? Select No to save in a temporary file.');
         else
             answerx = 'Yes';
         end
@@ -260,13 +250,10 @@ function callback_scTenifoldCko(src, ~)
         end
     end
 
-    fn=fullfile(wkdir, 'merged_embeds.h5');
-
-    eb = h5read(fn,'/data')';
-
+    fn=fullfile(wkdir, 'merged_embeds.h5');    
+    eb = h5read(fn,'/data')';    
     n = height(eb);
-    sl = n / 4;
-
+    sl = n / 4;    
     % Split the eb into four equal-length sub-ebs
     a = eb(1:sl,:);
     b = eb(sl+1:2*sl,:);
@@ -282,11 +269,16 @@ function callback_scTenifoldCko(src, ~)
     %[sce.g(x) sce.g(y)]
 
     [T] = ten.i_dr(a, c, sce.g, true);
-    outfile = sprintf('outfile_%s_expression_changes.csv',celltype1);
+    T = addvars(T, repelem(celltype1, height(T), 1), 'Before', 1);
+    T.Properties.VariableNames{'Var1'} = 'celltype';
+    outfile = sprintf('outfile_expression_changes_in_%s.csv', ...
+        matlab.lang.makeValidName(celltype1));
     writetable(T, outfile);
 
     [T] = ten.i_dr(b, d, sce.g, true);
-    outfile = sprintf('outfile_%s_expression_changes.csv',celltype1);
+    T = addvars(T, repelem(celltype2, height(T), 1), 'Before', 1);
+    T.Properties.VariableNames{'Var1'} = 'celltype';   
+    outfile = sprintf('outfile_expression_changes_in_%s.csv', ...
+        matlab.lang.makeValidName(celltype2));
     writetable(T, outfile);
-
 end

+pkg/i_addwd2script.m

@@ -5,16 +5,17 @@ function i_addwd2script(scriptfile, targetdir, ftype)
     if ~exist(targetdir, 'dir'), error('pkg.i_addwd2script error.'); end
 
     S = fileread(scriptfile);
-
+    [~,b,c]=fileparts(scriptfile);
+
     switch ftype
         case 'R'
             x = sprintf('setwd("%s")', strrep(targetdir,'\','\\'));
             S = [x, newline, S];
-            outscriptfile = fullfile(targetdir,'script.R');
+            outscriptfile = fullfile(targetdir, [b,c]);
         case 'python'
             x = sprintf('os.chdir("%s")', strrep(targetdir,'\','\\'));
             S = ['import os', newline, x, newline, S];
-            outscriptfile = fullfile(targetdir,'script.py');
+            outscriptfile = fullfile(targetdir, [b,c]);
     end
 
 

+run/external/py_scTenifoldCko/script_path.py

@@ -0,0 +1,78 @@
+#script_path
+#import os
+import sys
+#abspath = os.path.abspath(__file__)
+#dname = os.path.dirname(abspath)
+# os.chdir(dname)
+
+import scanpy as sc
+import scTenifoldXct as st
+from scTenifoldXct.dataLoader import build_adata
+import pandas as pd
+import numpy as np
+import h5py
+import scipy
+from scipy import sparse
+
+twosided = 1
+with h5py.File('X1.mat', 'r') as f:
+    if 'targetgid' in f:
+        targetgid = f['targetgid'][0]
+
+adata1 = build_adata("X1.mat", "g1.txt", "c1.txt", delimiter=',', meta_cell_cols=['cell_type'], transpose=False)
+print('Input read.............1')
+xct1 = st.scTenifoldXct(data = adata1, 
+                    source_celltype = 'Source',
+                    target_celltype = 'Target',
+                    obs_label = "cell_type",
+                    rebuild_GRN = False,
+                    GRN_file_dir = './1',
+                    verbose = True)
+
+adata2 = build_adata("X2.mat", "g2.txt", "c2.txt", delimiter=',', meta_cell_cols=['cell_type'], transpose=False)
+print('Input read.............2')
+xct2 = st.scTenifoldXct(data = adata2, 
+                    source_celltype = 'Source',
+                    target_celltype = 'Target',
+                    obs_label = "cell_type",
+                    rebuild_GRN = False,
+                    GRN_file_dir = './2',
+                    verbose = True)
+
+xct2=xct2.Knk(targetgid)
+
+XCTs = st.merge_scTenifoldXct(xct1, xct2)
+emb = XCTs.get_embeds(train = True)
+
+with h5py.File('merged_embeds.h5', 'w') as h5file:
+    h5file.create_dataset('data', data=emb)
+
+XCTs.nn_aligned_diff(emb) 
+xcts_pairs_diff = XCTs.chi2_diff_test(pval = 1.0)
+pd.DataFrame(xcts_pairs_diff).to_csv('output1.txt',index=False,header=True)
+
+# if sys.argv[1]=="2":
+if twosided==1:    
+    xct1 = st.scTenifoldXct(data = adata1, 
+                        source_celltype = 'Target',
+                        target_celltype = 'Source',
+                        obs_label = "cell_type",
+                        rebuild_GRN = False,
+                        GRN_file_dir = './1',
+                        verbose = True)
+
+    xct2 = st.scTenifoldXct(data = adata2, 
+                        source_celltype = 'Target',
+                        target_celltype = 'Source',
+                        obs_label = "cell_type",
+                        rebuild_GRN = False,
+                        GRN_file_dir = './2',
+                        verbose = True)
+
+    xct2=xct2.Knk(targetgid)
+    XCTs = st.merge_scTenifoldXct(xct1, xct2)
+    emb = XCTs.get_embeds(train = True)
+    XCTs.nn_aligned_diff(emb) 
+    xcts_pairs_diff = XCTs.chi2_diff_test(pval = 1.0)
+    pd.DataFrame(xcts_pairs_diff).to_csv('output2.txt',index=False,header=True)
+

+run/py_scTenifoldCko_type.m → +run/py_scTenifoldCko_gene.m

@@ -1,4 +1,4 @@
-function [T] = py_scTenifoldCko_type(sce, celltype1, celltype2, targetg, ...
+function [T] = py_scTenifoldCko_gene(sce, celltype1, celltype2, targetg, ...
                                 targettype, wkdir, ...
                                 isdebug, prepare_input_only)
 
@@ -127,7 +127,7 @@
 
     fw = gui.gui_waitbar([], [], 'Step 4 of 4: Running scTenifoldXct.py...');
 
-codefullpath = fullfile(codepth,'script.py');
+codefullpath = fullfile(codepth,'script_gene.py');
 pkg.i_addwd2script(codefullpath, wkdir, 'python');