Merge pull request SysBioChalmers#489 from SysBioChalmers/feat/misc

feat/fix: miscellaneous
qqlaoxia · Jun 21, 2023 · 9468a22 · 9468a22
2 parents 8793679 + d5864f5
commit 9468a22
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -5,8 +5,4 @@
 
 **I hereby confirm that I have:**
 <!-- Note: replace [ ] with [X] to check the box -->
-
-- [ ] Tested my code on my own machine
-- [ ] Followed the [development guidelines](https://github.com/SysBioChalmers/RAVEN/wiki/DevGuidelines).
-- [ ] Selected `devel` as a target branch
-- [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/RAVEN) about this PR
+- [ ] Selected `develop` as a target branch
diff --git a/core/analyzeSampling.m b/core/analyzeSampling.m
@@ -72,7 +72,7 @@
             Zf(i)=Zf(i)*-1;
         end
     end
-    
+
     I=Zf(i)/Tex(i);
     if I<0
         pM(i)=erf(abs(Zf(i)));
@@ -95,14 +95,14 @@
     for i=1:10
         fprintf([num2str(J(i)) '\t' num2str(I(i)) '\n']);
     end
-    
+
     %The top 10 hits in the first category
     [I, J]=sort(pH,'descend');
     fprintf('\nReactions which change in expression but not in flux\nReaction\tProbability\n');
     for i=1:10
         fprintf([num2str(J(i)) '\t' num2str(I(i)) '\n']);
     end
-    
+
     %The top 10 hits in the first category
     [I, J]=sort(pM,'descend');
     fprintf('\nReactions which change in flux but not in expression, or in opposed directions in flux and expression\nReaction\tProbability\n');
@@ -111,3 +111,63 @@
     end
 end
 end
+
+function p = tcdf(t,v,uflag)
+% TCDF Student's T cumulative distribution function (cdf).
+%
+% P = TCDF(X,V) computes the cdf for Student's T distribution
+% with V degrees of freedom, at the values in X. V must be a
+% scalar or have the same size as T.
+%
+% P = TCDF(X,V,'upper') computes it for the upper tail instead
+% of the lower tail.
+%
+% This is an alternative to the TCDF function that is implemented
+% in the Matlab statistics toolbox. This version originates from
+% http://www.statsci.org/matlab/statbox.html and originally was called TP.
+% It has been renamed to TCDF for drop-in compatibility with the Matlab
+% version.
+%
+% Gordon Smyth, University of Queensland, [email protected]
+% 3 Apr 97
+%
+% NaN compatible - Markus Bauer and Eric Maris, FCDC
+% 27 Jan 2005
+%
+% fixed bug concerning NaN compatibility
+% 21 Aug 2006, Markus Siegel
+%
+% added support for upper tail, see http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3045
+% 13 Jan 2016, Robert Oostenveld
+%
+% taken from https://github.com/fieldtrip/fieldtrip/blob/master/external/stats/tcdf.m
+% 05 May 2022
+
+if v <= 0, error('Degrees of freedom must be positive.'); end
+
+% resize v if necessary
+if all(size(v)==1)
+    v = ones(size(t))*v;
+end
+
+%check for NaN's - don't do calculations on them, give those out as NaNs
+if any( not(isfinite(t(:))) | not(isfinite(v(:))) )
+    sel = find(isfinite(t) & isfinite(v));
+    x=nan(size(t));
+    p=nan(size(t));
+    x(sel) = t(sel).^2 ./ (v(sel) + t(sel).^2) ;
+    p(sel) = 0.5 .* ( 1 + sign(t(sel)) .* betainc( x(sel), 0.5, 0.5*v(sel) ) );
+else
+    x = t.^2 ./ (v + t.^2) ;
+    p = 0.5 .* ( 1 + sign(t) .* betainc( x, 0.5, 0.5*v ) );
+end
+
+if nargin==3
+    if strcmp(uflag, 'upper')
+        % compute it for the upper tail instead of the lower tail
+        p = 1-p;
+    else
+        error('incorrect specification of uflag');
+    end
+end
+end
diff --git a/core/printOrange.m b/core/printOrange.m
@@ -0,0 +1,16 @@
+function printOrange(stringToPrint)
+% printOrange
+%   Print orange-colored stringToPrint to the MATLAB Command Window. Only
+%   if MATLAB is open with GUI, does not work with command-line MATLAB.
+%
+% Input: 
+%   stringToPrint   string that should be printed in orange color
+%
+% Usage: printOrange(stringToPrint)
+try useDesktop = usejava('desktop'); catch, useDesktop = false; end
+if useDesktop
+    fprintf(['[\b' stringToPrint,']\b'])
+else
+    fprintf(stringToPrint)
+end
+end
diff --git a/doc/core/analyzeSampling.html b/doc/core/analyzeSampling.html
@@ -67,7 +67,9 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
 </ul>
 <!-- crossreference -->
 
-
+<h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
+<ul style="list-style-image:url(../matlabicon.gif)">
+<li><a href="#_sub1" class="code">function p = tcdf(t,v,uflag)</a></li></ul>
 
 <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
 <div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function scores=analyzeSampling(Tex, df, solutionsA, solutionsB, printResults)</a>
@@ -137,23 +139,23 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0065     I=mB(i)/mA(i);
 0066     <span class="keyword">if</span> I&lt;0
 0067         pM(i)=erf(abs(Zf(i)));
-0068         pH(i)=(1-pM(i))*(2*tcdf(abs(Tex(i)),df)-1);
+0068         pH(i)=(1-pM(i))*(2*<a href="#_sub1" class="code" title="subfunction p = tcdf(t,v,uflag)">tcdf</a>(abs(Tex(i)),df)-1);
 0069         pR(i)=0;
 0070     <span class="keyword">else</span>
 0071         <span class="keyword">if</span> mB(i)&lt;0
 0072             Zf(i)=Zf(i)*-1;
 0073         <span class="keyword">end</span>
 0074     <span class="keyword">end</span>
-0075     
+0075 
 0076     I=Zf(i)/Tex(i);
 0077     <span class="keyword">if</span> I&lt;0
 0078         pM(i)=erf(abs(Zf(i)));
-0079         pH(i)=(1-pM(i))*(2*tcdf(abs(Tex(i)),df)-1);
+0079         pH(i)=(1-pM(i))*(2*<a href="#_sub1" class="code" title="subfunction p = tcdf(t,v,uflag)">tcdf</a>(abs(Tex(i)),df)-1);
 0080         pR(i)=0;
 0081     <span class="keyword">else</span>
-0082         pR(i)=erf(abs(Zf(i)))*(2*tcdf(abs(Tex(i)),df)-1);
-0083         pH(i)=(2*tcdf(abs(Tex(i)),df)-1)*(1-erf(abs(Zf(i))));
-0084         pM(i)=erf(abs(Zf(i)))*(1-(2*tcdf(abs(Tex(i)),df)-1));
+0082         pR(i)=erf(abs(Zf(i)))*(2*<a href="#_sub1" class="code" title="subfunction p = tcdf(t,v,uflag)">tcdf</a>(abs(Tex(i)),df)-1);
+0083         pH(i)=(2*<a href="#_sub1" class="code" title="subfunction p = tcdf(t,v,uflag)">tcdf</a>(abs(Tex(i)),df)-1)*(1-erf(abs(Zf(i))));
+0084         pM(i)=erf(abs(Zf(i)))*(1-(2*<a href="#_sub1" class="code" title="subfunction p = tcdf(t,v,uflag)">tcdf</a>(abs(Tex(i)),df)-1));
 0085     <span class="keyword">end</span>
 0086 <span class="keyword">end</span>
 0087 
@@ -167,22 +169,82 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0095     <span class="keyword">for</span> i=1:10
 0096         fprintf([num2str(J(i)) <span class="string">'\t'</span> num2str(I(i)) <span class="string">'\n'</span>]);
 0097     <span class="keyword">end</span>
-0098     
+0098 
 0099     <span class="comment">%The top 10 hits in the first category</span>
 0100     [I, J]=sort(pH,<span class="string">'descend'</span>);
 0101     fprintf(<span class="string">'\nReactions which change in expression but not in flux\nReaction\tProbability\n'</span>);
 0102     <span class="keyword">for</span> i=1:10
 0103         fprintf([num2str(J(i)) <span class="string">'\t'</span> num2str(I(i)) <span class="string">'\n'</span>]);
 0104     <span class="keyword">end</span>
-0105     
+0105 
 0106     <span class="comment">%The top 10 hits in the first category</span>
 0107     [I, J]=sort(pM,<span class="string">'descend'</span>);
 0108     fprintf(<span class="string">'\nReactions which change in flux but not in expression, or in opposed directions in flux and expression\nReaction\tProbability\n'</span>);
 0109     <span class="keyword">for</span> i=1:10
 0110         fprintf([num2str(J(i)) <span class="string">'\t'</span> num2str(I(i)) <span class="string">'\n'</span>]);
 0111     <span class="keyword">end</span>
 0112 <span class="keyword">end</span>
-0113 <span class="keyword">end</span></pre></div>
+0113 <span class="keyword">end</span>
+0114 
+0115 <a name="_sub1" href="#_subfunctions" class="code">function p = tcdf(t,v,uflag)</a>
+0116 <span class="comment">% TCDF Student's T cumulative distribution function (cdf).</span>
+0117 <span class="comment">%</span>
+0118 <span class="comment">% P = TCDF(X,V) computes the cdf for Student's T distribution</span>
+0119 <span class="comment">% with V degrees of freedom, at the values in X. V must be a</span>
+0120 <span class="comment">% scalar or have the same size as T.</span>
+0121 <span class="comment">%</span>
+0122 <span class="comment">% P = TCDF(X,V,'upper') computes it for the upper tail instead</span>
+0123 <span class="comment">% of the lower tail.</span>
+0124 <span class="comment">%</span>
+0125 <span class="comment">% This is an alternative to the TCDF function that is implemented</span>
+0126 <span class="comment">% in the Matlab statistics toolbox. This version originates from</span>
+0127 <span class="comment">% http://www.statsci.org/matlab/statbox.html and originally was called TP.</span>
+0128 <span class="comment">% It has been renamed to TCDF for drop-in compatibility with the Matlab</span>
+0129 <span class="comment">% version.</span>
+0130 <span class="comment">%</span>
+0131 <span class="comment">% Gordon Smyth, University of Queensland, [email protected]</span>
+0132 <span class="comment">% 3 Apr 97</span>
+0133 <span class="comment">%</span>
+0134 <span class="comment">% NaN compatible - Markus Bauer and Eric Maris, FCDC</span>
+0135 <span class="comment">% 27 Jan 2005</span>
+0136 <span class="comment">%</span>
+0137 <span class="comment">% fixed bug concerning NaN compatibility</span>
+0138 <span class="comment">% 21 Aug 2006, Markus Siegel</span>
+0139 <span class="comment">%</span>
+0140 <span class="comment">% added support for upper tail, see http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3045</span>
+0141 <span class="comment">% 13 Jan 2016, Robert Oostenveld</span>
+0142 <span class="comment">%</span>
+0143 <span class="comment">% taken from https://github.com/fieldtrip/fieldtrip/blob/master/external/stats/tcdf.m</span>
+0144 <span class="comment">% 05 May 2022</span>
+0145 
+0146 <span class="keyword">if</span> v &lt;= 0, error(<span class="string">'Degrees of freedom must be positive.'</span>); <span class="keyword">end</span>
+0147 
+0148 <span class="comment">% resize v if necessary</span>
+0149 <span class="keyword">if</span> all(size(v)==1)
+0150     v = ones(size(t))*v;
+0151 <span class="keyword">end</span>
+0152 
+0153 <span class="comment">%check for NaN's - don't do calculations on them, give those out as NaNs</span>
+0154 <span class="keyword">if</span> any( not(isfinite(t(:))) | not(isfinite(v(:))) )
+0155     sel = find(isfinite(t) &amp; isfinite(v));
+0156     x=nan(size(t));
+0157     p=nan(size(t));
+0158     x(sel) = t(sel).^2 ./ (v(sel) + t(sel).^2) ;
+0159     p(sel) = 0.5 .* ( 1 + sign(t(sel)) .* betainc( x(sel), 0.5, 0.5*v(sel) ) );
+0160 <span class="keyword">else</span>
+0161     x = t.^2 ./ (v + t.^2) ;
+0162     p = 0.5 .* ( 1 + sign(t) .* betainc( x, 0.5, 0.5*v ) );
+0163 <span class="keyword">end</span>
+0164 
+0165 <span class="keyword">if</span> nargin==3
+0166     <span class="keyword">if</span> strcmp(uflag, <span class="string">'upper'</span>)
+0167         <span class="comment">% compute it for the upper tail instead of the lower tail</span>
+0168         p = 1-p;
+0169     <span class="keyword">else</span>
+0170         error(<span class="string">'incorrect specification of uflag'</span>);
+0171     <span class="keyword">end</span>
+0172 <span class="keyword">end</span>
+0173 <span class="keyword">end</span></pre></div>
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