This is a static copy of a profile report

Home

phased_and_unphased_color_definitions (1 call, 0.030 sec)
Generated 14-Nov-2016 07:47:09 using cpu time.
script in file /home/user/dev/ymap/scripts_seqModules/phased_and_unphased_color_definitions.m
Copy to new window for comparing multiple runs

Parents (calling functions)

Function NameFunction TypeCalls
LOH_hapmap_v4function1
Lines where the most time was spent

Line NumberCodeCallsTotal Time% TimeTime Plot
280
alternate_color_5of9      = od...
10 s0%
279
alternate_color_6of9      = od...
10 s0%
278
alternate_color_7of9      = od...
10 s0%
277
alternate_color_8of9      = od...
10 s0%
276
alternate_color_9of9      = ho...
10 s0%
All other lines  0.030 s100.0%
Totals  0.030 s100% 
Children (called functions)
No children
Code Analyzer results
Line numberMessage
252Terminate statement with semicolon to suppress output (within a script).
Coverage results
Show coverage for parent directory
Total lines in function280
Non-code lines (comments, blank lines)59
Code lines (lines that can run)221
Code lines that did run156
Code lines that did not run65
Coverage (did run/can run)70.59 %
Function listing
time 
calls 
 line
      1 
   1 
colorNoData = [1.0     1.0     1.0    ]; % used when no data is available for the bin. 
      1 
   2 
colorInit   = [0.5     0.5     0.5    ]; % external; used in blending at ends of chr. 
      1 
   3 
colorHET    = [0.66667 0.66667 0.66667]; % near 1:1 ratio SNPs 
      1 
   4 
colorHOM    = [1.0     0.0     0.0    ]; % Hom SNPs; 
   5 

      1 
   6 
if (useHapmap == true) 
   7 
	%% Load color names defined for hapmap;
   8 
	colorsFile = [hapmapDir 'colors.txt'];
   9 
	if (exist(colorsFile,'file') == 2)
  10 
		colors_fid = fopen([main_dir 'users/' hapmapUser '/hapmaps/' hapmap '/colors.txt'], 'r');
  11 
		% The swapped colors are to correct for a polarity mistake in the python preprocessing steps.
  12 
		%    correcting the error there would require reprocessing all current datasets.
  13 
		colorA_string = fgetl(colors_fid);
  14 
		colorB_string = fgetl(colors_fid);
  15 
		fclose(colors_fid);
  16 
	else
  17 
		colorA_string = 'red';
  18 
		colorB_string = 'red';
  19 
	end;
  20 
	fprintf(['\nHapmap colors:\n\tcolorA = ' colorA_string '\n\tcolorB = ' colorB_string '\n\n']);
  21 
	switch colorA_string
  22 
		case 'deep pink'
  23 
			homolog_a_color = [1.0 0.0 0.5];
  24 
		case 'magenta'
  25 
			homolog_a_color = [1.0 0.0 1.0];
  26 
		case 'electric indigo'
  27 
			homolog_a_color = [0.5 0.0 1.0];
  28 
		case 'blue'
  29 
			homolog_a_color = [0.0 0.0 1.0];
  30 
		case 'dodger blue'
  31 
			homolog_a_color = [0.0 0.5 1.0];
  32 
		case 'cyan'
  33 
			homolog_a_color = [0.0 1.0 1.0];
  34 
		case 'spring green'
  35 
			homolog_a_color = [0.0 1.0 0.5];
  36 
		case 'green'
  37 
			homolog_a_color = [0.0 1.0 0.0];
  38 
		case 'chartreuse'
  39 
			homolog_a_color = [0.5 1.0 0.0];
  40 
		case 'yellow'
  41 
			homolog_a_color = [1.0 1.0 0.0];
  42 
		case 'dark orange'
  43 
			homolog_a_color = [1.0 0.5 0.0];
  44 
		case 'red'
  45 
			homolog_a_color = [1.0 0.0 0.0];
  46 
	end;
  47 
	switch colorB_string
  48 
		case 'deep pink'
  49 
			homolog_b_color = [1.0 0.0 0.5];
  50 
		case 'magenta'
  51 
			homolog_b_color = [1.0 0.0 1.0];
  52 
		case 'electric indigo'
  53 
			homolog_b_color = [0.5 0.0 1.0];
  54 
		case 'blue'
  55 
			homolog_b_color = [0.0 0.0 1.0];
  56 
		case 'dodger blue'
  57 
			homolog_b_color = [0.0 0.5 1.0];
  58 
		case 'cyan'
  59 
			homolog_b_color = [0.0 1.0 1.0];
  60 
		case 'spring green'
  61 
			homolog_b_color = [0.0 1.0 0.5];
  62 
		case 'green'
  63 
			homolog_b_color = [0.0 1.0 0.0];
  64 
		case 'chartreuse'
  65 
			homolog_b_color = [0.5 1.0 0.0];
  66 
		case 'yellow'
  67 
			homolog_b_color = [1.0 1.0 0.0];
  68 
		case 'dark orange'
  69 
			homolog_b_color = [1.0 0.5 0.0];
  70 
		case 'red'
  71 
			homolog_b_color = [1.0 0.0 0.0];
  72 
	end;
      1 
  73 
else 
  74 
	% Haplotype map is not in use.
      1 
  75 
	if (strcmp(project,hapmap) == 1) 
  76 
		% The 'project' is the same as the 'hapmap'/'parent'.
  77 
		homolog_a_color = [0.66667 0.66667 0.66667];
  78 
		homolog_b_color = [0.66667 0.66667 0.66667];
      1 
  79 
	else 
  80 
		% The 'project' is different than the 'hapmap'/'parent'.
      1 
  81 
		homolog_a_color = [1.0 0.0 0.0]; 
      1 
  82 
		homolog_b_color = [1.0 0.0 0.0]; 
      1 
  83 
	end; 
      1 
  84 
end; 
      1 
  85 
hom_color    = [1.0     0.0     0.0    ]; % completely homozygous. 
      1 
  86 
het_color    = [0.66667 0.66667 0.66667]; % heterozygous. 
      1 
  87 
oddHet_color = [0.0     1.0     0.0    ]; % non-heterozygous data that isn't 100 hom. 
  88 

  89 

  90 
%%%%%%%% phased data colors.
  91 

  92 
% haploid colors.
      1 
  93 
colorA          = homolog_a_color; 
      1 
  94 
colorB          = homolog_b_color; 
  95 
% diploid colors.
      1 
  96 
colorAA         = homolog_a_color; 
      1 
  97 
colorAB         = het_color; 
      1 
  98 
colorBB         = homolog_b_color; 
  99 
% triploid colors.
      1 
 100 
colorAAA        = homolog_a_color; 
      1 
 101 
colorAAB        = homolog_a_color*2/3 + homolog_b_color*1/3; 
      1 
 102 
colorABB        = homolog_a_color*1/3 + homolog_b_color*2/3; 
      1 
 103 
colorBBB        = homolog_b_color; 
 104 
% tetraploid colors.
      1 
 105 
colorAAAA       = homolog_a_color; 
      1 
 106 
colorAAAB       = homolog_a_color*3/4 + homolog_b_color*1/4; 
      1 
 107 
colorAABB       = het_color; 
      1 
 108 
colorABBB       = homolog_a_color*1/4 + homolog_b_color*3/4; 
      1 
 109 
colorBBBB       = homolog_b_color; 
 110 
% pentaploid colors.
      1 
 111 
colorAAAAA      = homolog_a_color; 
      1 
 112 
colorAAAAB      = homolog_a_color*4/5 + homolog_b_color*1/5; 
      1 
 113 
colorAAABB      = homolog_a_color*3/5 + homolog_b_color*2/5; 
      1 
 114 
colorAABBB      = homolog_a_color*2/5 + homolog_b_color*3/5; 
      1 
 115 
colorABBBB      = homolog_a_color*1/5 + homolog_b_color*4/5; 
      1 
 116 
colorBBBBB      = homolog_b_color; 
 117 
% hexaploid colors.
      1 
 118 
colorAAAAAA     = homolog_a_color; 
      1 
 119 
colorAAAAAB     = homolog_a_color*5/6 + homolog_b_color*1/6; 
      1 
 120 
colorAAAABB     = homolog_a_color*4/6 + homolog_b_color*2/6; 
      1 
 121 
colorAAABBB     = het_color; 
      1 
 122 
colorAABBBB     = homolog_a_color*2/6 + homolog_b_color*4/6; 
      1 
 123 
colorABBBBB     = homolog_a_color*1/6 + homolog_b_color*5/6; 
      1 
 124 
colorBBBBBB     = homolog_b_color; 
 125 
% heptaploid colors.
      1 
 126 
colorAAAAAAA    = homolog_a_color; 
      1 
 127 
colorAAAAAAB    = homolog_a_color*6/7 + homolog_b_color*1/7; 
      1 
 128 
colorAAAAABB    = homolog_a_color*5/7 + homolog_b_color*2/7; 
      1 
 129 
colorAAAABBB    = homolog_a_color*4/7 + homolog_b_color*3/7; 
      1 
 130 
colorAAABBBB    = homolog_a_color*3/7 + homolog_b_color*4/7; 
      1 
 131 
colorAABBBBB    = homolog_a_color*2/7 + homolog_b_color*5/7; 
      1 
 132 
colorABBBBBB    = homolog_a_color*1/7 + homolog_b_color*6/7; 
      1 
 133 
colorBBBBBBB    = homolog_b_color; 
 134 
% octaploid colors.
      1 
 135 
colorAAAAAAAA   = homolog_a_color; 
      1 
 136 
colorAAAAAAAB   = homolog_a_color*7/8 + homolog_b_color*1/8; 
      1 
 137 
colorAAAAAABB   = homolog_a_color*6/8 + homolog_b_color*2/8; 
      1 
 138 
colorAAAAABBB   = homolog_a_color*5/8 + homolog_b_color*3/8; 
      1 
 139 
colorAAAABBBB   = het_color; 
      1 
 140 
colorAAABBBBB   = homolog_a_color*3/8 + homolog_b_color*5/8; 
      1 
 141 
colorAABBBBBB   = homolog_a_color*2/8 + homolog_b_color*6/8; 
      1 
 142 
colorABBBBBBB   = homolog_a_color*1/8 + homolog_b_color*7/8; 
      1 
 143 
colorBBBBBBBB   = homolog_b_color; 
 144 
% nonaploid colors.
      1 
 145 
colorAAAAAAAAA  = homolog_a_color; 
      1 
 146 
colorAAAAAAAAB  = homolog_a_color*8/9 + homolog_b_color*1/9; 
      1 
 147 
colorAAAAAAABB  = homolog_a_color*7/9 + homolog_b_color*2/9; 
      1 
 148 
colorAAAAAABBB  = homolog_a_color*6/9 + homolog_b_color*3/9; 
      1 
 149 
colorAAAAABBBB  = homolog_a_color*5/9 + homolog_b_color*4/9; 
      1 
 150 
colorAAAABBBBB  = homolog_a_color*4/9 + homolog_b_color*5/9; 
      1 
 151 
colorAAABBBBBB  = homolog_a_color*3/9 + homolog_b_color*6/9; 
      1 
 152 
colorAABBBBBBB  = homolog_a_color*2/9 + homolog_b_color*7/9; 
      1 
 153 
colorABBBBBBBB  = homolog_a_color*1/9 + homolog_b_color*8/9; 
      1 
 154 
colorBBBBBBBBB  = homolog_b_color; 
 155 

 156 

 157 
%%%%%%%% unphased colors.
 158 

 159 
% haploid colors.
      1 
 160 
unphased_color_1of1 = hom_color; 
 161 
% diploid colors.
      1 
 162 
unphased_color_2of2 = hom_color; 
      1 
 163 
unphased_color_1of2 = het_color; 
 164 
% triploid colors.
      1 
 165 
unphased_color_3of3 = hom_color; 
      1 
 166 
unphased_color_2of3 = hom_color*1/3 + het_color*2/3; 
 167 
% tetraploid colors.
      1 
 168 
unphased_color_4of4 = hom_color; 
      1 
 169 
unphased_color_3of4 = hom_color*1/2 + het_color*1/2; 
      1 
 170 
unphased_color_2of4 = het_color; 
 171 
% pentaploid colors.
      1 
 172 
unphased_color_5of5 = hom_color; 
      1 
 173 
unphased_color_4of5 = hom_color*3/5 + het_color*2/5; 
      1 
 174 
unphased_color_3of5 = hom_color*1/5 + het_color*4/5; 
 175 
% hexaploid colors.
      1 
 176 
unphased_color_6of6 = hom_color; 
      1 
 177 
unphased_color_5of6 = hom_color*4/6 + het_color*2/6; 
      1 
 178 
unphased_color_4of6 = hom_color*2/6 + het_color*4/6; 
      1 
 179 
unphased_color_3of6 = het_color; 
 180 
% heptaploid colors.
      1 
 181 
unphased_color_7of7 = hom_color; 
      1 
 182 
unphased_color_6of7 = hom_color*5/7 + het_color*2/7; 
      1 
 183 
unphased_color_5of7 = hom_color*3/7 + het_color*4/7; 
      1 
 184 
unphased_color_4of7 = hom_color*1/7 + het_color*6/7; 
 185 
% octaploid colors.
      1 
 186 
unphased_color_8of8 = hom_color; 
      1 
 187 
unphased_color_7of8 = hom_color*6/8 + het_color*2/8; 
      1 
 188 
unphased_color_6of8 = hom_color*4/8 + het_color*4/8; 
      1 
 189 
unphased_color_5of8 = hom_color*2/8 + het_color*6/8; 
      1 
 190 
unphased_color_4of8 = het_color; 
 191 
% nonaploid colors.
      1 
 192 
unphased_color_9of9 = hom_color; 
      1 
 193 
unphased_color_8of9 = hom_color*7/9 + het_color*2/9; 
      1 
 194 
unphased_color_7of9 = hom_color*5/9 + het_color*4/9; 
      1 
 195 
unphased_color_6of9 = hom_color*3/9 + het_color*6/9; 
      1 
 196 
unphased_color_5of9 = hom_color*1/9 + het_color*8/9; 
 197 

 198 

 199 
%%%%%%%% colors for no parent.
 200 

 201 
% haploid colors.
      1 
 202 
noparent_color_1of1 = colorNoData; 
 203 
% diploid colors.
      1 
 204 
noparent_color_2of2 = colorNoData; 
      1 
 205 
noparent_color_1of2 = het_color; 
 206 
% triploid colors.
      1 
 207 
noparent_color_3of3 = colorNoData; 
      1 
 208 
noparent_color_2of3 = colorNoData*1/3 + het_color*2/3; 
 209 
% tetraploid colors.
      1 
 210 
noparent_color_4of4 = colorNoData; 
      1 
 211 
noparent_color_3of4 = colorNoData*1/2 + het_color*1/2; 
      1 
 212 
noparent_color_2of4 = het_color; 
 213 
% pentaploid colors.
      1 
 214 
noparent_color_5of5 = colorNoData; 
      1 
 215 
noparent_color_4of5 = colorNoData*3/5 + het_color*2/5; 
      1 
 216 
noparent_color_3of5 = colorNoData*1/5 + het_color*4/5; 
 217 
% hexaploid colors.
      1 
 218 
noparent_color_6of6 = colorNoData; 
      1 
 219 
noparent_color_5of6 = colorNoData*4/6 + het_color*2/6; 
      1 
 220 
noparent_color_4of6 = colorNoData*2/6 + het_color*4/6; 
      1 
 221 
noparent_color_3of6 = het_color; 
 222 
% heptaploid colors.
      1 
 223 
noparent_color_7of7 = colorNoData; 
      1 
 224 
noparent_color_6of7 = colorNoData*5/7 + het_color*2/7; 
      1 
 225 
noparent_color_5of7 = colorNoData*3/7 + het_color*4/7; 
      1 
 226 
noparent_color_4of7 = colorNoData*1/7 + het_color*6/7; 
 227 
% octaploid colors.
      1 
 228 
noparent_color_8of8 = colorNoData; 
      1 
 229 
noparent_color_7of8 = colorNoData*6/8 + het_color*2/8; 
      1 
 230 
noparent_color_6of8 = colorNoData*4/8 + het_color*4/8; 
      1 
 231 
noparent_color_5of8 = colorNoData*2/8 + het_color*6/8; 
      1 
 232 
noparent_color_4of8 = het_color; 
 233 
% nonaploid colors.
      1 
 234 
noparent_color_9of9 = colorNoData; 
      1 
 235 
noparent_color_8of9 = colorNoData*7/9 + het_color*2/9; 
      1 
 236 
noparent_color_7of9 = colorNoData*5/9 + het_color*4/9; 
      1 
 237 
noparent_color_6of9 = colorNoData*3/9 + het_color*6/9; 
      1 
 238 
noparent_color_5of9 = colorNoData*1/9 + het_color*8/9; 
 239 

 240 

 241 
%%%%%%%% alternate colors for use with hapmap or parent.
 242 

 243 
% haploid colors.
      1 
 244 
alternate_color_1of1      = hom_color; 
 245 
% diploid colors.
      1 
 246 
alternate_color_2of2      = hom_color; 
      1 
 247 
alternate_color_1of2      = het_color; 
 248 
% triploid colors.
      1 
 249 
alternate_color_3of3      = hom_color; 
      1 
 250 
alternate_color_2of3      = oddHet_color; 
 251 
% tetraploid colors.
      1 
 252 
alternate_color_4of4      = hom_color 
      1 
 253 
alternate_color_3of4      = oddHet_color; 
      1 
 254 
alternate_color_2of4      = het_color; 
 255 
% pentaploid colors.
      1 
 256 
alternate_color_5of5      = hom_color; 
      1 
 257 
alternate_color_4of5      = oddHet_color; 
      1 
 258 
alternate_color_3of5      = oddHet_color; 
 259 
% hexaploid colors.
      1 
 260 
alternate_color_6of6      = hom_color; 
      1 
 261 
alternate_color_5of6      = oddHet_color; 
      1 
 262 
alternate_color_4of6      = oddHet_color; 
      1 
 263 
alternate_color_3of6      = het_color; 
 264 
% heptaploid colors.
      1 
 265 
alternate_color_7of7      = hom_color; 
      1 
 266 
alternate_color_6of7      = oddHet_color; 
      1 
 267 
alternate_color_5of7      = oddHet_color; 
      1 
 268 
alternate_color_4of7      = oddHet_color; 
 269 
% octaploid colors.
      1 
 270 
alternate_color_8of8      = hom_color; 
      1 
 271 
alternate_color_7of8      = oddHet_color; 
      1 
 272 
alternate_color_6of8      = oddHet_color; 
      1 
 273 
alternate_color_5of8      = oddHet_color; 
      1 
 274 
alternate_color_4of8      = het_color; 
 275 
% nonaploid colors.
      1 
 276 
alternate_color_9of9      = hom_color; 
      1 
 277 
alternate_color_8of9      = oddHet_color; 
      1 
 278 
alternate_color_7of9      = oddHet_color; 
      1 
 279 
alternate_color_6of9      = oddHet_color; 
      1 
 280 
alternate_color_5of9      = oddHet_color;