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cailab-tamu · Apr 4, 2020 · c9cf8f5 · c9cf8f5
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Showing 20 changed files with 531 additions and 4,118 deletions.
diff --git a/MATLAB/i_dr.m b/MATLAB/i_dr.m
@@ -0,0 +1,27 @@
+function [T]=i_dr(aln0,aln1,genelist,doplot)
+    if nargin<4, doplot=false; end
+    drdist=vecnorm(aln0-aln1,2,2).^2;
+    FC=drdist./mean(drdist);
+    pValues=chi2cdf(FC,1,'upper');
+    pAdjusted = mafdr(pValues,'BHFDR',true);
+    if size(genelist,1)==1, genelist=genelist'; end
+    sortid=[1:length(genelist)]';
+    T=table(sortid,genelist,drdist,FC,pValues,pAdjusted);
+    T = sortrows(T,'drdist','descend');
+    if doplot
+        pd = makedist('Gamma','a',0.5,'b',2);
+        qqplot(FC,pd);
+        [~,i]=sort(FC);
+        dt = datacursormode;
+        dt.UpdateFcn = {@i_myupdatefcn1,genelist(i)};
+    end
+end
+
+function txt = i_myupdatefcn1(~,event_obj,g)
+% Customizes text of data tips
+% pos = event_obj.Position;
+idx = event_obj.DataIndex;
+% i_plotsiglegene(idx,g);
+txt = {g(idx)};
+end
+
diff --git a/MATLAB/i_nc.m b/MATLAB/i_nc.m
@@ -0,0 +1,18 @@
+function  [XM0,XM1]=i_nc(X0,X1)
+    n=size(X0,1);
+    XM0=zeros(n,n,10);
+    XM1=zeros(n,n,10);
+    for k=1:10
+        fprintf('network...%d of 10\n',k);
+
+        Xrep=X0(:,randperm(size(X0,2)));
+        A=sc_pcnetpar(Xrep(:,1:500),3,false);
+        A=A./max(abs(A(:)));        
+        XM0(:,:,k)=A.*(abs(A)>quantile(abs(A(:)),0.95));
+
+        Xrep=X1(:,randperm(size(X1,2)));
+        A=sc_pcnetpar(Xrep(:,1:500),3,false);    
+        A=A./max(abs(A(:)));
+        XM1(:,:,k)=A.*(abs(A)>quantile(abs(A(:)),0.95));
+    end
+end
diff --git a/MATLAB/sctenifoldnet_m.m b/MATLAB/sctenifoldnet_m.m
@@ -13,49 +13,19 @@
     pw1=fileparts(which(mfilename));
     cd(pw1);
     addpath('thirdparty\tensor_toolbox-v3.1\');
+    cd(pw0);
+    if exist('sc_pcnet.m','file')~=2
+        error('scGEAToolbox installation is required. Link: https://github.com/jamesjcai/scGEAToolbox');
+    end    
 
-    n=size(X0,1);
-    XM0=zeros(n,n,10);
-    XM1=zeros(n,n,10);
-    for k=1:10
-        fprintf('network...%d of 10\n',k);
-
-        Xrep=X0(:,randperm(size(X0,2)));
-        A=sc_pcnetpar(Xrep(:,1:500),3,false);
-        A=A./max(abs(A(:)));        
-        XM0(:,:,k)=A.*(abs(A)>quantile(abs(A(:)),0.95));
-
-        Xrep=X1(:,randperm(size(X1,2)));
-        A=sc_pcnetpar(Xrep(:,1:500),3,false);    
-        A=A./max(abs(A(:)));
-        XM1(:,:,k)=A.*(abs(A)>quantile(abs(A(:)),0.95));
-    end
-
+    X0=sc_norm(X0,"type","libsize");
+    X1=sc_norm(X1,"type","libsize");
+
+    [XM0,XM1]=i_nc(X0,X1);
     A0=i_td(XM0,2);
     A1=i_td(XM1,2);
-
     [aln0,aln1]=i_ma(A0,A1);
-    drdist=vecnorm(aln0-aln1,2,2).^2;
-    FC=drdist./mean(drdist);
-    pValues=chi2cdf(FC,1,'upper');
-    pAdjusted = mafdr(pValues,'BHFDR',true);
-    if size(genelist,1)==1, genelist=genelist'; end
-    T=table(genelist,drdist,FC,pValues,pAdjusted);    
-    if doplot
-        pd = makedist('Gamma','a',0.5,'b',2);
-        qqplot(FC,pd);
-        [~,i]=sort(FC);
-        dt = datacursormode;
-        dt.UpdateFcn = {@i_myupdatefcn1,genelist(i)};
-    end
-    cd(pw0);
-end
-
-function txt = i_myupdatefcn1(~,event_obj,g)
-% Customizes text of data tips
-% pos = event_obj.Position;
-idx = event_obj.DataIndex;
-% i_plotsiglegene(idx,g);
-txt = {g(idx)};
+    T=i_dr(aln0,aln1,genelist,doplot);
+
 end
 
diff --git a/MATLAB/test/X.txt b/MATLAB/test/X.txt
diff --git a/MATLAB/test/X0.csv b/MATLAB/test/X0.csv
diff --git a/MATLAB/test/X1.csv b/MATLAB/test/X1.csv
diff --git a/MATLAB/test/Xtensor.csv b/MATLAB/test/Xtensor.csv
diff --git a/MATLAB/test/Y.txt b/MATLAB/test/Y.txt
diff --git a/MATLAB/test/Ytensor.csv b/MATLAB/test/Ytensor.csv
diff --git a/MATLAB/test/example10xdata_1877g.mat b/MATLAB/test/example10xdata_1877g.mat
diff --git a/MATLAB/test/example10xdata_8842g.mat b/MATLAB/test/example10xdata_8842g.mat
diff --git a/MATLAB/test/example_main_code.m b/MATLAB/test/example_main_code.m
diff --git a/MATLAB/test/examplenetworks.mat b/MATLAB/test/examplenetworks.mat
diff --git a/MATLAB/test/genelist.txt b/MATLAB/test/genelist.txt
@@ -0,0 +1,150 @@
+Rpl18-ps2
+Ifi27l2a
+Park7
+mt-Nd1
+Srsf7
+Rps12
+Psma7
+Gm26522
+Rpl18a-ps1
+Mt1
+Smim1
+Timm8b
+Cox14
+Klf13
+RP23-123N23.5
+Psme2b
+RP23-228E2.8
+Marc2
+RP24-217J7.2
+Aplp2
+Smdt1
+Ppp1r15a
+Mcl1
+Spry1
+Ctsz
+Scgb1c1
+Polr2e
+Jund
+Chd3
+Emd
+Tmem208
+Ywhaz
+Tinagl1
+RP23-407K8.3
+AC102906.1
+Lamtor5
+Gabarapl2
+RP23-356D13.4
+Klf4
+Srsf6
+Srsf2
+mt-Nd5
+Selenbp1
+Anxa3
+Bri3
+Cox4i1
+B4galt1
+Set
+RP24-417N21.2
+RP23-21C14.1
+Cyb5r3
+Rbm39
+Cxcl16
+Csrp1
+Mrpl14
+Sftpa1
+Stard10
+Fkbp1a
+Tubb4b
+Gdi2
+Nupr1
+Cat
+AC155158.1
+Calr
+Cyb5b
+Sgms1
+Tubb5
+Emp2
+Ssr1
+H2-DMb1
+Anxa1
+Adk
+Tspan11
+Spg21
+Atpif1
+Rpl26
+Socs2
+Ndufc1
+Mal
+Lyz2
+Hspb1
+Spcs2
+Rpl12
+Rpl3-ps1
+Anxa4
+Snrpb
+Rplp1
+Rpl13a
+Rpp21
+Tmed2
+Pfdn1
+Pnisr
+Btf3
+Dynll2
+Nop10
+Acaa2
+Imp3
+Rpl38
+RP24-190H19.2
+Cd200
+Rpl17
+Cd47
+Eef1a1
+Jun
+Cmtm8
+Rpl28-ps3
+Arpp19
+Fkbp2
+Atp1a1
+Elovl1
+Rpl10
+RP23-41B18.5
+Ptma
+H2afz
+Snrpd2
+Rpl27a
+RP23-426M5.1
+Anxa6
+Pdlim1
+Sec62
+Tmem258
+Canx
+Ywhab
+Rps15a-ps8
+Prr15l
+Txnip
+Rn18s-rs5
+Oaz1
+Car8
+Ier3
+Tmem50a
+Rpl19
+Sfpq
+RP23-387F9.3
+Rpl32
+Dpm3
+Lrg1
+Srrm2
+Akr1a1
+Echs1
+Rab9
+Epas1
+Rpl31-ps8
+mt-Nd4
+Eef1g
+Atp5g1
+Hmgb2
+Elob
+Rps13-ps1
+Nnat
diff --git a/MATLAB/test/i_startwt_tensorout.m b/MATLAB/test/i_startwt_tensorout.m
diff --git a/MATLAB/test/perturbation.R b/MATLAB/test/perturbation.R
diff --git a/MATLAB/test/perturbation.txt b/MATLAB/test/perturbation.txt
diff --git a/MATLAB/test/s0_process_data.m b/MATLAB/test/s0_process_data.m