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Load_size_info (2 calls, 0.010 sec)
Generated 14-Nov-2016 07:47:12 using cpu time.
function in file /home/user/dev/ymap/scripts_seqModules/Load_size_info.m
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Parents (calling functions)

Function NameFunction TypeCalls
LOH_hapmap_v4function1
allelic_ratios_WGseqfunction1
Lines where the most time was spent

Line NumberCodeCallsTotal Time% TimeTime Plot
89
fprintf('chr font size:%d, axi...
20.010 s100.0%
140
end
20 s0%
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fprintf('\n-------------------...
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fprintf('chr font size:%d, axi...
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fprintf('height:%d px, width:%...
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All other lines  0 s0%
Totals  0.010 s100% 
Children (called functions)

Function NameFunction TypeCallsTotal Time% TimeTime Plot
verLessThanfunction40 s0%
Self time (built-ins, overhead, etc.)  0.010 s100.0%
Totals  0.010 s100% 
Code Analyzer results
No Code Analyzer messages.
Coverage results
Show coverage for parent directory
Total lines in function140
Non-code lines (comments, blank lines)60
Code lines (lines that can run)80
Code lines that did run68
Code lines that did not run12
Coverage (did run/can run)85.00 %
Function listing
time 
calls 
 line
   1 
function [linear_fig_height,linear_fig_width,linear_left_padding,linear_chr_gap,linear_chr_max_width,linear_height...
   2 
            ,linear_base,rotate,linear_chr_font_size,linear_axis_font_size,linear_gca_font_size,stacked_fig_height,stacked_fig_width,...
   3 
            stacked_chr_font_size,stacked_title_size,stacked_axis_font_size,gca_stacked_font_size,stacked_copy_font_size,max_chrom_label_size] = Load_size_info(chr_in_use,num_chrs,chr_label,chr_size)
      2 
   4 
fprintf('\n---------------------------------Load_size_info.m started---------------------------------------------------\n'); 
   5 

   6 
%% calculating data used to determine size 
   7 

   8 
% calculate the number of chrs used
      2 
   9 
num_chrs_used = 0; 
      2 
  10 
for chr = 1:num_chrs 
     18 
  11 
	if (chr_in_use(chr) == 1) 
     16 
  12 
        num_chrs_used = num_chrs_used + 1; 
     16 
  13 
	end; 
     18 
  14 
end; 
      2 
  15 
fprintf('num_chrs_used - %d\n',num_chrs_used); 
  16 

  17 
% calculating the maximum length of chromosome label size for the height of linear figure
      2 
  18 
max_chrom_label_size = 1; 
      2 
  19 
for chr = 1:num_chrs 
     18 
  20 
    if (chr_in_use(chr) == 1) 
     16 
  21 
        if (numel(chr_label{chr}) > numel(max_chrom_label_size)) 
     16 
  22 
            max_chrom_label_size = numel(chr_label{chr}); 
     16 
  23 
        end; 
     16 
  24 
    end; 
     18 
  25 
end; 
      2 
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fprintf('max_chrom_label_size - %d\n',max_chrom_label_size); 
  27 

  28 
%% global definitions
  29 
% the default dpi used by the system, in matlab no screen mode before 2014 it's 72dpi, and in later versions 150dpi
      2 
  30 
if verLessThan('matlab','8.4') 
  31 
    % -- Code to run in MATLAB R2014a and earlier here --
  32 
    system_dpi = 72; 
      2 
  33 
else 
  34 
    % -- Code to run in MATLAB R2014b and later here --
      2 
  35 
    system_dpi = 150;  
      2 
  36 
end; 
      2 
  37 
fprintf('using %d dpi\n',system_dpi); 
  38 

  39 
%% linear figure
      2 
  40 
fprintf('-----------------------------------Linear Figure -----------------------------------------------\n'); 
  41 
% setting size for linear figure
      2 
  42 
linear_fig_plot_height = 130; % the height of each chromosom in the figure in px (including y-axis) 
      2 
  43 
linear_fig_charc_height = 20; % the size to be allocated in px for each character in the label  
  44 

      2 
  45 
linear_fig_height_px = linear_fig_plot_height + linear_fig_charc_height*max_chrom_label_size; % the total height of the linear figure in px 
  46 
% normalize height according to dpi
      2 
  47 
linear_fig_height = linear_fig_height_px / system_dpi; 
  48 

      2 
  49 
linear_fig_width_px = 2400; 
      2 
  50 
linear_fig_width = linear_fig_width_px / system_dpi; 
  51 

  52 
% base value in matlab (the scaling here is from 0 to 1 and represent
  53 
% relative position
      2 
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linear_left_padding    = 0.02;               % left margin 
      2 
  55 
linear_right_padding   = 0.02;               % right margin 
      2 
  56 
linear_total_gap     = 0.07;               % the size in precentage for total gap accross all figure 
      2 
  57 
linear_cartoon_height_px = 111;            % the size of the chromosome cartoon in pixles (without y-axis) for proper scaling 
      2 
  58 
linear_chr_gap  = linear_total_gap/(num_chrs-1);  % gaps between chr subfigures. 
      2 
  59 
linear_chr_max_width = 1 - linear_total_gap - linear_left_padding - linear_right_padding;  % width for all chromosomes across figure.  1.00 - leftMargin - rightMargin - subfigure gaps. 
      2 
  60 
linear_height        = linear_cartoon_height_px/ linear_fig_height_px; % the size  
      2 
  61 
linear_base          = 0.1; 
  62 

  63 
% setting rotation
  64 
% if there are more than5 charcters in label 90 degrees rotation, else
  65 
% rotating accroding to lowest chromosome size
  66 
% 45 degrees boundries 
      2 
  67 
lower_boundary = 0.10; 
      2 
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upper_boundary = 0.25; 
  69 
% removing zero enteries in chromosom sizes
      2 
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chr_size_cleaned = chr_size(chr_size ~= 0); 
  71 
% calculate ration between smallest chromosome size to highest
      2 
  72 
ratio = min(chr_size_cleaned)/max(chr_size_cleaned); 
      2 
  73 
rotate = 0; 
      2 
  74 
if (max_chrom_label_size > 5) 
  75 
    rotate = 90;
      2 
  76 
elseif (lower_boundary <= ratio && ratio <= upper_boundary) 
  77 
    rotate = 45;
      2 
  78 
elseif(ratio < lower_boundary) 
  79 
    rotate = 90;
  80 
end;
  81 

  82 
% font definitions
      2 
  83 
linear_axis_font_size = 10; 
      2 
  84 
linear_gca_font_size = 12; 
      2 
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linear_chr_font_size = 12; 
  86 

      2 
  87 
fprintf('linear figure paramters:\n'); 
      2 
  88 
fprintf('height:%d px, width:%d px, rotate:%d\n',linear_fig_height_px,linear_fig_width_px,rotate); 
  0.01 
      2 
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fprintf('chr font size:%d, axis font size:%d px, gca font size:%d\n',linear_chr_font_size,linear_axis_font_size,linear_gca_font_size); 
  90 

  91 
%% stacked figure %%
      2 
  92 
fprintf('-----------------------------------Stacked Figure -----------------------------------------------\n'); 
  93 

      2 
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stacked_plot_height = 205; % size in pixels of each cartoon height including gap 
      2 
  95 
stacked_fig_height_px = stacked_plot_height*num_chrs_used; % the total height of the linear figure in px 
  96 
% normalize height according to dpi
      2 
  97 
stacked_fig_height = stacked_fig_height_px / system_dpi; 
  98 

      2 
  99 
stacked_fig_width_px = 2400; 
      2 
 100 
stacked_fig_width = stacked_fig_width_px / system_dpi; 
 101 

 102 
% if the matlab version is less then 2016a then use scaling since the font doesn't scale well
      2 
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if verLessThan('matlab','9.0') 
 104 
    % -- Code to run in MATLAB R2016a and earlier here --
 105 
    % the size of the stacked title normalized to 8 chromosomes (that appear
 106 
    % right), 8 is what appeared correct in candida albicans, just increasing size makes figure look not good
      2 
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    stacked_title_size = 18*(8/num_chrs_used); 
 108 
    % the size of axis values in stacked figure
      2 
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    stacked_axis_font_size = 10*(8/num_chrs_used); 
 110 
    % the size of gca font in stacked mode
      2 
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    gca_stacked_font_size = 12*(8/num_chrs_used); 
 112 
    % the size of chromosome text in stacked figure
      2 
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    stacked_chr_font_size = 16*(8/num_chrs_used); 
 114 
    % the size of the copy beside figure in stacked
      2 
 115 
    stacked_copy_font_size = 20*(8/num_chrs_used); 
 116 
else
 117 
    % -- Code to run in MATLAB R2016a and later here --
 118 
    stacked_title_size = 18;
 119 
    % the size of axis values in stacked figure
 120 
    stacked_axis_font_size = 10;
 121 
    % the size of gca font in stacked mode
 122 
    gca_stacked_font_size = 12;
 123 
    % the size of chromosome text in stacked figure
 124 
    stacked_chr_font_size = 16;
 125 
    % the size of the copy beside figure in stacked
 126 
    stacked_copy_font_size = 20;
 127 
end;
 128 

 129 

 130 

      2 
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fprintf('stacked figure paramters:\n'); 
      2 
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fprintf('height:%d px, width:%d px, title size:%d\n',stacked_fig_height_px,stacked_fig_width_px,stacked_title_size); 
      2 
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fprintf('chr font size:%d, axis font size:%d px, gca font size:%d\n',stacked_chr_font_size,stacked_axis_font_size,gca_stacked_font_size); 
 134 

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      2 
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fprintf('\n---------------------------------Load_size_info.m ended---------------------------------------------------\n'); 
 138 

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      2 
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end