fix some bugs in figure generation scripts

Author: sergarcia

README.rst

@@ -3,10 +3,10 @@
 
         __  ___          ________     ____
        /  |/  /___  ____/ / ____/__  / / /
-      / /|_/ / __ \/ __  / /   / _ \/ / / 
-     / /  / / /_/ / /_/ / /___/  __/ / /  
-    /_/  /_/\____/\__,_/\____/\___/_/_/   
-    ==================================            
+      / /|_/ / __ \/ __  / /   / _ \/ / /
+     / /  / / /_/ / /_/ / /___/  __/ / /
+    /_/  /_/\____/\__,_/\____/\___/_/_/
+    ==================================
 
 This is the repository for the ModCell2 modular strain design framework.
 
@@ -25,10 +25,10 @@ Installation
 ------------
 Download or clone this repository, then add simply add the ModCell2 folder to your MATLAB path by running
 ::
-   
+
    addpath(genpath(['<parent-directory>', filesep, 'ModCell2']))
 
-Where <parent-directory> depends on your system. To verify your installation execute :code:`run_all_tests.m`. :warning: Make sure the Requierements_ are met. :warning:.
+Where <parent-directory> depends on your system. To verify your installation execute :code:`run_all_tests.m`. :warning: Make sure the Requierements_ are met. :warning:. You may need to run `initCobraToolbox` once within Matlab for certain methods to work correctly.
 
 Quick start
 ------------

problems/ecoli-gem/mip/flux_analysis/flux_analysis.m

@@ -28,7 +28,7 @@
     'Pentyl pentanoate'};
 prodnet.prod_name = good_prod_name;
 %% Set prodnet to target design
-[T1, ~, design_vars] = format_output(fullfile(modcell_path,'problems','ecoli-gem','mip','flux_analysis_2','a6_b1_optimized_modules.csv'),prodnet, 'wGCP');
+[T1, ~, design_vars] = format_output(fullfile(modcell_path,'problems','ecoli-gem','mip','flux_analysis','a6_b1_optimized_modules.csv'),prodnet, 'wGCP');
 i=1;
 prodnet.set_module_and_deleted_variables(design_vars(i).Z,design_vars(i).y)
 

problems/ecoli-gem/mip/flux_analysis/generate_pe.m

@@ -29,7 +29,7 @@
     'Pentyl pentanoate'};
 prodnet.prod_name = good_prod_name;
 %% Set prodnet to target design
-[T1, ~, design_vars] = format_output(fullfile(modcell_path,'problems','ecoli-gem','mip','flux_analysis_2','a6_b1_optimized_modules.csv'),prodnet, 'wGCP');
+[T1, ~, design_vars] = format_output(fullfile(modcell_path,'problems','ecoli-gem','mip','flux_analysis','a6_b1_optimized_modules.csv'),prodnet, 'wGCP');
 i=1;
 %prodnet.set_module_and_deleted_variables(design_vars(i).Z,design_vars(i).y)
 prodnet.reset_wild_type_state();
@@ -48,6 +48,6 @@
 X_TICK_LABEL_DIGITS = 2;
 
 ResAnalysis.plot_yield_vs_growth_s(model_array, ko_array, prod_id, solution_id,...
-    'min_obj_val',0,'plot_type','overlap', 'n_rows',4, 'n_cols',5, ...
+    'min_obj_val',0,'plot_type','overlap', 'n_rows',5, 'n_cols',4, ...
     'xticks_values', [0:0.05:0.15], 'all_yticks',false, 'all_xticks', false,...
     'grid', true)

problems/ecoli-gem/mip/flux_analysis/optimize_production_modules.m

@@ -57,10 +57,10 @@
     prodnet.set_module_and_deleted_variables(pm(i).Z,y);
     wgcp(:,i) = prodnet.calc_design_objectives('wGCP');
 end
-%% 
+%%
 names = {pm(:).id};
 names{1} = 'None';
-T = array2table(wgcp); 
+T = array2table(wgcp);
 T.Properties.VariableNames = names;
 T.Properties.RowNames = prodnet.prod_id;
 T
@@ -73,7 +73,7 @@
         default{1} = 'None';
     end
     fprintf('\t (Default: %s)\n', default{1})
-    no_module = wgcp(k,1); 
+    no_module = wgcp(k,1);
     max_ind = find(wgcp(k,:) == max(wgcp(k,:))); % Only if increase is significant!
     for i =1:length(max_ind)
         if isempty(pm(max_ind(i)).id)
@@ -88,7 +88,7 @@
 
 %% Edit file and load:
 [T2, ~, design_vars2] = format_output(fullfile(modcell_path,'problems','ecoli-gem',...
-    'mip','flux_analysis_2','a6_b1_optimized_modules.csv'),prodnet, 'wGCP');
+    'mip','flux_analysis','a6_b1_optimized_modules.csv'),prodnet, 'wGCP');
 i=1;
 
 %% Plot of  maximum theoretical yield vs module performance
@@ -142,4 +142,4 @@
 set(gca,'YGrid','on')
 set_figure_defaults
 set(gcf, 'Units', 'Inches', 'Position', [0, 0, 4.5, 3])
-print(['yield_v.svg'],'-dsvg')
+print(['yield_v.svg'],'-dsvg')

src/@ResAnalysis/plot_yield_vs_growth_s.m

@@ -115,7 +115,7 @@ function plot_yield_vs_growth_s(model_array, ko_array, prod_id, solution_id, var
     mut_colors(4,:) = [255,255,0]./255; % yellow
     mut_colors(5,:) = [204, 0, 0]./255; % red dark    
 
-    mut_line_colors = mut_colors./inputs.line_color_divider;
+    mut_line_colors = mut_colors./inputs.line_color_factor;
     mut_line_colors(3,:) = mut_colors(3,:); % for NGP in the third case the line has to be bright
 
 end