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angle_plot_subfigures (8 calls, 0.947 sec)
Generated 14-Nov-2016 07:47:09 using cpu time.
script in file /home/user/dev/ymap/scripts_seqModules/angle_plot_subfigures.m
Copy to new window for comparing multiple runs

Parents (calling functions)

Function NameFunction TypeCalls
LOH_hapmap_v4function8
Lines where the most time was spent

Line NumberCodeCallsTotal Time% TimeTime Plot
265
area(coord3:coord4, segment_sm...
130.161 s17.0%
260
area(coord2:200, segment_smoot...
120.131 s13.8%
256
area(1:coord1, segment_smoothe...
120.131 s13.8%
275
plot([peaks(peak); peaks(peak)...
370.101 s10.6%
42
fprintf(['    copyNum      = '...
370.071 s7.4%
All other lines  0.353 s37.2%
Totals  0.947 s100% 
Children (called functions)

Function NameFunction TypeCallsTotal Time% TimeTime Plot
areafunction370.423 s44.7%
num2strfunction3440.141 s14.9%
subplotfunction120.071 s7.4%
newplotfunction620.060 s6.4%
holdfunction240.020 s2.1%
ylimfunction120 s0%
xlimfunction120 s0%
isholdfunction620 s0%
Self time (built-ins, overhead, etc.)  0.232 s24.5%
Totals  0.947 s100% 
Code Analyzer results
No Code Analyzer messages.
Coverage results
Show coverage for parent directory
Total lines in function285
Non-code lines (comments, blank lines)9
Code lines (lines that can run)276
Code lines that did run99
Code lines that did not run177
Coverage (did run/can run)35.87 %
Function listing
time 
calls 
 line
      8 
   5 
if (AnglePlot == true) 
      8 
   6 
	width      = 0.075; 
      8 
   7 
	height     = chr_height(chr); 
      8 
   8 
	bottom     = chr_posY(chr); 
      8 
   9 
	chr_length = chr_size(chr); 
      8 
  10 
	for segment = 1:length(chrCopyNum{chr}) 
  0.01 
     12 
  11 
		fprintf(['^^^     segment#    = ' num2str(segment) ':' num2str(length(chrCopyNum{chr})) '\n']); 
  12 

     12 
  13 
		if (segment == 1) % generate sublot for each segment. 
  0.05 
      8 
  14 
			subplot('Position',[0.03 bottom width (height/length(chrCopyNum{chr}))]); 
      4 
  15 
		else 
  0.02 
      4 
  16 
			subplot('Position',[0.03 (bottom+height/length(chrCopyNum{chr})*(segment-1)) width (height/length(chrCopyNum{chr}))]); 
      4 
  17 
		end; 
  18 

     12 
  19 
		peaks                     = chrSegment_peaks{              chr}{segment}; 
     12 
  20 
		mostLikelyGaussians       = chrSegment_mostLikelyGaussians{chr}{segment}; 
     12 
  21 
		actual_cutoffs            = chrSegment_actual_cutoffs{     chr}{segment}; 
     12 
  22 
		segment_smoothedHistogram = chrSegment_smoothed{           chr}{segment}; 
     12 
  23 
		segment_copyNum           = round(chrCopyNum{              chr}(segment)); 
     12 
  24 
		segment_chrBreaks         = chr_breaks{                    chr}(segment); 
  25 

     12 
  26 
		fprintf(['^^^     copyNum             = ' num2str(segment_copyNum)     '\n']); 
     12 
  27 
		fprintf(['^^^     peaks               = ' num2str(peaks)               '\n']); 
  0.01 
     12 
  28 
		fprintf(['^^^     mostLikelyGaussians = ' num2str(mostLikelyGaussians) '\n']); 
  0.01 
     12 
  29 
		fprintf(['^^^     actual_cutoffs      = ' num2str(actual_cutoffs)      '\n']); 
  30 

     12 
  31 
		copynum = round(chrCopyNum{chr}(segment)); 
     12 
  32 
		region_ = 0; 
  0.02 
     12 
  33 
		hold on; 
     12 
  34 
		for region = mostLikelyGaussians 
     37 
  35 
			region_ = region_+1; 
  36 
			% Define color of the histogram region.
     37 
  37 
			if (FillColors == true) 
  0.04 
     37 
  38 
				fprintf(['region_ #= ' num2str(region_) '\n']); 
     37 
  39 
				if (show_uncalibrated == true) 
  40 
					color = colorAB;
     37 
  41 
				else 
  0.07 
     37 
  42 
					fprintf(['    copyNum      = ' num2str(copynum) '\n']); 
     37 
  43 
					if (copynum == 0) %deletion or error 
     37 
  44 
					elseif (copynum == 1) %monosomy 
      2 
  45 
						if (apply_phasing == true) 
      2 
  46 
							if (region == 2);     color = colorB; 
      1 
  47 
							else                  color = colorA; 
      1 
  48 
							end; 
  49 
						else
  50 
							if (region == 2);     color = unphased_color_1of1;
  51 
							else                  color = unphased_color_1of1;
  52 
							end;
  53 
						end;
      2 
  54 
						if (segment == 1) 
  55 
							set(gca,'XTick',[0 200]);
  56 
							set(gca,'XTickLabel',{'a','b'});
  57 
						end;
     35 
  58 
					elseif (copynum == 2) %disomy 
     29 
  59 
						if (apply_phasing == true) 
     29 
  60 
							if (region == 3);     color = colorBB; 
     18 
  61 
							elseif (region == 2); color = colorAB; 
      9 
  62 
							else                  color = colorAA; 
      9 
  63 
							end; 
  64 
						else
  65 
							if (region == 3);     color = unphased_color_2of2;
  66 
							elseif (region == 2); color = unphased_color_1of2;
  67 
							else                  color = unphased_color_2of2;
  68 
							end;
  69 
						end;
     29 
  70 
						if (segment == 1) 
     23 
  71 
							set(gca,'XTick',0:100:200); 
  0.01 
     23 
  72 
							set(gca,'XTickLabel',{'a','ab','b'}); 
     23 
  73 
						end; 
      6 
  74 
					elseif (copynum == 3) %trisomy 
      6 
  75 
						if (apply_phasing == true) 
      6 
  76 
							if (region == 4);     color = colorBBB; 
      5 
  77 
							elseif (region == 3); color = colorABB; 
      3 
  78 
							elseif (region == 2); color = colorAAB; 
      1 
  79 
							else                  color = colorAAA; 
      1 
  80 
							end; 
  81 
						else
  82 
							if (region == 4);     color = unphased_color_3of3;
  83 
							elseif (region == 3); color = unphased_color_2of3;
  84 
							elseif (region == 2); color = unphased_color_2of3;
  85 
							else                  color = unphased_color_3of3;
  86 
							end;
  87 
						end;
      6 
  88 
						if (segment == 1) 
      4 
  89 
							set(gca,'XTick',[0 66.667 133.333 200]); 
      4 
  90 
							set(gca,'XTickLabel',{'a','aab','abb','b'}); 
      4 
  91 
						end; 
  92 
					elseif (copynum == 4) %tetrasomy
  93 
						if (apply_phasing == true)
  94 
							if (region == 5);     color = colorBBBB;
  95 
							elseif (region == 4); color = colorABBB;
  96 
							elseif (region == 3); color = colorAABB;
  97 
							elseif (region == 2); color = colorAAAB;
  98 
							else                  color = colorAAAA;
  99 
							end;
 100 
						else
 101 
							if (region == 5);     color = unphased_color_4of4;
 102 
							elseif (region == 4); color = unphased_color_3of4;
 103 
							elseif (region == 3); color = unphased_color_2of4;
 104 
							elseif (region == 2); color = unphased_color_3of4;
 105 
							else                  color = unphased_color_4of4;
 106 
							end;
 107 
						end;
 108 
						if (segment == 1)
 109 
							set(gca,'XTick',0:50:200);
 110 
							set(gca,'XTickLabel',{'a', '3:1', '2:2', '1:3' 'b'});
 111 
						end;
 112 
					elseif (copynum == 5) %pentasomy
 113 
						if (apply_phasing == true)
 114 
							if (region == 6);     color = colorBBBBB;
 115 
							elseif (region == 5); color = colorABBBB;
 116 
							elseif (region == 4); color = colorAABBB;
 117 
							elseif (region == 3); color = colorAAABB;
 118 
							elseif (region == 2); color = colorAAAAB;
 119 
							else                  color = colorAAAAA;
 120 
							end;
 121 
						else
 122 
							if (region == 6);     color = unphased_color_5of5;
 123 
							elseif (region == 5); color = unphased_color_4of5;
 124 
							elseif (region == 4); color = unphased_color_3of5;
 125 
							elseif (region == 3); color = unphased_color_3of5;
 126 
							elseif (region == 2); color = unphased_color_4of5;
 127 
							else                  color = unphased_color_5of5;
 128 
							end;
 129 
						end;
 130 
						if (segment == 1)
 131 
							set(gca,'XTick',0:40:200);
 132 
							set(gca,'XTickLabel',{'a', '4:!', '3:2', '2:3', '1:4' 'b'});
 133 
						end;
 134 
					elseif (copynum == 6) %hexasomy
 135 
						if (apply_phasing == true)
 136 
							if (region == 7);     color = colorBBBBBB;
 137 
							elseif (region == 6); color = colorABBBBB;
 138 
							elseif (region == 5); color = colorAABBBB;
 139 
							elseif (region == 4); color = colorAAABBB;
 140 
							elseif (region == 3); color = colorAAAABB;
 141 
							elseif (region == 2); color = colorAAAAAB;
 142 
							else                  color = colorAAAAAA;
 143 
							end;
 144 
						else
 145 
							if (region == 7);     color = unphased_color_6of6;
 146 
							elseif (region == 6); color = unphased_color_5of6;
 147 
							elseif (region == 5); color = unphased_color_4of6;
 148 
							elseif (region == 4); color = unphased_color_3of6;
 149 
							elseif (region == 3); color = unphased_color_4of6;
 150 
							elseif (region == 2); color = unphased_color_5of6;
 151 
							else                  color = unphased_color_6of6;
 152 
							end;
 153 
						end;
 154 
						if (segment == 1)
 155 
							set(gca,'XTick',0:33.333:200);
 156 
							set(gca,'XTickLabel',{'a', '5:1', '4:2', '3:3', '2:4', '1:5' 'b'});
 157 
						end;
 158 
					elseif (copynum == 7) %heptasomy
 159 
						if (apply_phasing == true)
 160 
							if (region == 8);     color = colorBBBBBBB;
 161 
							elseif (region == 7); color = colorABBBBBB;
 162 
							elseif (region == 6); color = colorAABBBBB;
 163 
							elseif (region == 5); color = colorAAABBBB;
 164 
							elseif (region == 4); color = colorAAAABBB;
 165 
							elseif (region == 3); color = colorAAAAABB;
 166 
							elseif (region == 2); color = colorAAAAAAB;
 167 
							else                  color = colorAAAAAAA;
 168 
							end;
 169 
						else
 170 
							if (region == 8);     color = unphased_color_7of7;
 171 
							elseif (region == 7); color = unphased_color_6of7;
 172 
							elseif (region == 6); color = unphased_color_5of7;
 173 
							elseif (region == 5); color = unphased_color_4of7;
 174 
							elseif (region == 4); color = unphased_color_4of7;
 175 
							elseif (region == 3); color = unphased_color_5of7;
 176 
							elseif (region == 2); color = unphased_color_6of7;
 177 
							else                  color = unphased_color_7of7;
 178 
							end;
 179 
						end;
 180 
						if (segment == 1)
 181 
							set(gca,'XTick',0:28.571:200);
 182 
							set(gca,'XTickLabel',{'a', '', '5:2', '', '', '2:5', '' 'b'});
 183 
						end;
 184 
					elseif (copynum == 8)  %octasomy
 185 
						if (apply_phasing == true)
 186 
							if (region == 9);     color = colorBBBBBBBB;
 187 
							elseif (region == 8); color = colorABBBBBBB;
 188 
							elseif (region == 7); color = colorAABBBBBB;
 189 
							elseif (region == 6); color = colorAAABBBBB;
 190 
							elseif (region == 5); color = colorAAAABBBB;
 191 
							elseif (region == 4); color = colorAAAAABBB;
 192 
							elseif (region == 3); color = colorAAAAAABB;
 193 
							elseif (region == 2); color = colorAAAAAAAB;
 194 
							else                  color = colorAAAAAAAA;
 195 
							end;
 196 
						else
 197 
							if (region == 9);     color = unphased_color_8of8;
 198 
							elseif (region == 8); color = unphased_color_7of8;
 199 
							elseif (region == 7); color = unphased_color_6of8;
 200 
							elseif (region == 6); color = unphased_color_5of8;
 201 
							elseif (region == 5); color = unphased_color_4of8;
 202 
							elseif (region == 4); color = unphased_color_5of8;
 203 
							elseif (region == 3); color = unphased_color_6of8;
 204 
							elseif (region == 2); color = unphased_color_7of8;
 205 
							else                  color = unphased_color_8of8;
 206 
							end;
 207 
						end;
 208 
						if (segment == 1)
 209 
							set(gca,'XTick',0:22.222:200);
 210 
							set(gca,'XTickLabel',{'a', '', '6:2', '', '4:4', '', '2:6', '' 'b'});
 211 
						end;
 212 
					else % (copynum >= 9) %nonasomy
 213 
						if (apply_phasing == true)
 214 
							if (region == 10);    color = colorBBBBBBBBB;
 215 
							elseif (region == 9); color = colorABBBBBBBB;
 216 
							elseif (region == 8); color = colorAABBBBBBB;
 217 
							elseif (region == 7); color = colorAAABBBBBB;
 218 
							elseif (region == 6); color = colorAAAABBBBB;
 219 
							elseif (region == 5); color = colorAAAAABBBB;
 220 
							elseif (region == 4); color = colorAAAAAABBB;
 221 
							elseif (region == 3); color = colorAAAAAAABB;
 222 
							elseif (region == 2); color = colorAAAAAAAAB;
 223 
							else                  color = colorAAAAAAAAA;
 224 
							end;
 225 
						else
 226 
							if (region == 10);    color = unphased_color_9of9;
 227 
							elseif (region == 9); color = unphased_color_8of9;
 228 
							elseif (region == 8); color = unphased_color_7of9;
 229 
							elseif (region == 7); color = unphased_color_6of9;
 230 
							elseif (region == 6); color = unphased_color_5of9;
 231 
							elseif (region == 5); color = unphased_color_5of9;
 232 
							elseif (region == 4); color = unphased_color_6of9;
 233 
							elseif (region == 3); color = unphased_color_7of9;
 234 
							elseif (region == 2); color = unphased_color_8of9;
 235 
							else                  color = unphased_color_9of9;
 236 
							end;
 237 
						end;
 238 
						if (segment == 1)
 239 
							set(gca,'XTick',0:20:200);
 240 
							set(gca,'XTickLabel',{'a', '', '', '6:3', '', '', '3:6', '', '', 'b'});
 241 
						end;
 242 
					end;
     37 
 243 
				end; 
 244 
			else
 245 
				color = colorAB;
 246 
			end;
 247 

  0.02 
     37 
 248 
			fprintf(['    mostLikelyGaussian   = ' num2str(region) '\n']); 
     37 
 249 
			if (length(mostLikelyGaussians) <= 1) 
 250 
				% draw entire smoothed histogram.
 251 
				area(1:200,segment_smoothedHistogram(1:200),'FaceColor',color,'EdgeColor',color);
     37 
 252 
			else 
 253 
				% draw segment of smoothed histogram corresponding to region.
     37 
 254 
				if (region_ == 1) % first region in list. 
     12 
 255 
					coord1 = max(min(round(actual_cutoffs(region_))+1, 200), 1); 
  0.13 
     12 
 256 
					area(1:coord1, segment_smoothedHistogram(1:coord1), 'FaceColor',color,'EdgeColor',color); 
     12 
 257 
					fprintf(['    angleplotCoordinates = 1:' num2str(coord1) '\n']); 
  0.02 
     25 
 258 
				elseif (region_ == length(mostLikelyGaussians)) % last region in list. 
     12 
 259 
					coord2 = max(min(round(actual_cutoffs(region_-1))+1, 200), 1); 
  0.13 
     12 
 260 
					area(coord2:200, segment_smoothedHistogram(coord2:200), 'FaceColor',color,'EdgeColor',color); 
  0.01 
     12 
 261 
					fprintf([' angleplotCoordinate = ' num2str(coord2) ':200\n']); 
     13 
 262 
				else 
     13 
 263 
					coord3 = max(min(round(actual_cutoffs(region_-1))+1, 200), 1); 
     13 
 264 
					coord4 = max(min(round(actual_cutoffs(region_  ))+1, 200), 1); 
  0.16 
     13 
 265 
					area(coord3:coord4, segment_smoothedHistogram(coord3:coord4), 'FaceColor',color,'EdgeColor',color); 
     13 
 266 
					fprintf(['    angleplotCoordinates = ' num2str(coord3) ':' num2str(coord4) '\n']); 
     13 
 267 
				end; 
     37 
 268 
			end; 
  0.05 
     37 
 269 
			fprintf(['    color = ' num2str(color) '   (colorA = [' num2str(colorA) ']; colorB = [' num2str(colorB) '])\n']); 
  0.02 
     37 
 270 
		end; 
 271 

     12 
 272 
		colorPeak   = [0.5 0.5 0.5]; % color of lines drawn at peak locations. 
     12 
 273 
		colorCutoff = [1.0 0.0 0.0]; % color of lines drawn at cutoffs between Gaussian fits. 
     12 
 274 
		for peak = 1:length(peaks) 
  0.10 
     37 
 275 
			plot([peaks(peak); peaks(peak)],[0; 1],'color',colorPeak); 
     37 
 276 
		end; 
     12 
 277 
		for cutoff = 1:length(actual_cutoffs) 
  0.06 
     25 
 278 
			plot([actual_cutoffs(cutoff); actual_cutoffs(cutoff)],[0; 1],'color',colorCutoff); 
     25 
 279 
		end; 
     12 
 280 
		set(gca,'FontSize',stacked_axis_font_size); 
     12 
 281 
		hold off; 
     12 
 282 
		set(gca,'YTick',[]); 
     12 
 283 
		if (segment ~= 1) 
      4 
 284 
			set(gca,'XTick',[]); 
      4 
 285 
		end; 
     12 
 286 
		xlim([0,200]); 
     12 
 287 
		ylim([0,1]); 
     12 
 288 
	end; 
      8 
 289 
end;