first commit for lipidomics

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto
+
+# Custom for Visual Studio
+*.cs     diff=csharp
+*.sln    merge=union
+*.csproj merge=union
+*.vbproj merge=union
+*.fsproj merge=union
+*.dbproj merge=union
+
+# Standard to msysgit
+*.doc	 diff=astextplain
+*.DOC	 diff=astextplain
+*.docx diff=astextplain
+*.DOCX diff=astextplain
+*.dot  diff=astextplain
+*.DOT  diff=astextplain
+*.pdf  diff=astextplain
+*.PDF	 diff=astextplain
+*.rtf	 diff=astextplain
+*.RTF	 diff=astextplain

.gitignore

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+#################
+## Eclipse
+#################
+
+*.pydevproject
+.project
+.metadata
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.classpath
+.settings/
+.loadpath
+
+# External tool builders
+.externalToolBuilders/
+
+# Locally stored "Eclipse launch configurations"
+*.launch
+
+# CDT-specific
+.cproject
+
+# PDT-specific
+.buildpath
+
+
+#################
+## Visual Studio
+#################
+
+## Ignore Visual Studio temporary files, build results, and
+## files generated by popular Visual Studio add-ons.
+
+# User-specific files
+*.suo
+*.user
+*.sln.docstates
+
+# Build results
+
+[Dd]ebug/
+[Rr]elease/
+x64/
+build/
+[Bb]in/
+[Oo]bj/
+
+# MSTest test Results
+[Tt]est[Rr]esult*/
+[Bb]uild[Ll]og.*
+
+*_i.c
+*_p.c
+*.ilk
+*.meta
+*.obj
+*.pch
+*.pdb
+*.pgc
+*.pgd
+*.rsp
+*.sbr
+*.tlb
+*.tli
+*.tlh
+*.tmp
+*.tmp_proj
+*.log
+*.vspscc
+*.vssscc
+.builds
+*.pidb
+*.log
+*.scc
+
+# Visual C++ cache files
+ipch/
+*.aps
+*.ncb
+*.opensdf
+*.sdf
+*.cachefile
+
+# Visual Studio profiler
+*.psess
+*.vsp
+*.vspx
+
+# Guidance Automation Toolkit
+*.gpState
+
+# ReSharper is a .NET coding add-in
+_ReSharper*/
+*.[Rr]e[Ss]harper
+
+# TeamCity is a build add-in
+_TeamCity*
+
+# DotCover is a Code Coverage Tool
+*.dotCover
+
+# NCrunch
+*.ncrunch*
+.*crunch*.local.xml
+
+# Installshield output folder
+[Ee]xpress/
+
+# DocProject is a documentation generator add-in
+DocProject/buildhelp/
+DocProject/Help/*.HxT
+DocProject/Help/*.HxC
+DocProject/Help/*.hhc
+DocProject/Help/*.hhk
+DocProject/Help/*.hhp
+DocProject/Help/Html2
+DocProject/Help/html
+
+# Click-Once directory
+publish/
+
+# Publish Web Output
+*.Publish.xml
+*.pubxml
+
+# NuGet Packages Directory
+## TODO: If you have NuGet Package Restore enabled, uncomment the next line
+#packages/
+
+# Windows Azure Build Output
+csx
+*.build.csdef
+
+# Windows Store app package directory
+AppPackages/
+
+# Others
+sql/
+*.Cache
+ClientBin/
+[Ss]tyle[Cc]op.*
+~$*
+*~
+*.dbmdl
+*.[Pp]ublish.xml
+*.pfx
+*.publishsettings
+
+# RIA/Silverlight projects
+Generated_Code/
+
+# Backup & report files from converting an old project file to a newer
+# Visual Studio version. Backup files are not needed, because we have git ;-)
+_UpgradeReport_Files/
+Backup*/
+UpgradeLog*.XML
+UpgradeLog*.htm
+
+# SQL Server files
+App_Data/*.mdf
+App_Data/*.ldf
+
+#############
+## Windows detritus
+#############
+
+# Windows image file caches
+Thumbs.db
+ehthumbs.db
+
+# Folder config file
+Desktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Mac crap
+.DS_Store
+
+
+#############
+## Python
+#############
+
+*.py[co]
+
+# Packages
+*.egg
+*.egg-info
+dist/
+build/
+eggs/
+parts/
+var/
+sdist/
+develop-eggs/
+.installed.cfg
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+
+#Translations
+*.mo
+
+#Mr Developer
+.mr.developer.cfg

Figure1.m

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+function [mol_parasite, mol_rbc, mol_uninfected, plot_mat ] = Figure1( parasite, rbc, uninfected, names, species )
+
+% parasite=DD2f_p_;    
+% rbc=DD2f_R_;
+% uninfected=uninf; 
+% names=DD2f_names; 
+
+
+groups=cell2mat(names(:,2)); 
+unique_=unique(groups); 
+cmap=[255/255 51/255 51/255; 0/255 204/255 102/255; 204/255 0/255 204/255];
+L_=length(unique_); 
+[r,c]=size(parasite);  
+mat=parasite; 
+mol_parasite=zeros(L_,c); 
+sum_mat=sum(parasite); 
+
+%find the mol%time for each lipid group
+for k=1:length(unique_);
+    indx=find(groups==unique_(k)); 
+    mat_=mat(indx,:); 
+    mat_species=sum(mat_); 
+    for j=1:c
+        mol_parasite(k,j)=mat_species(1,j)/sum_mat(1,j); 
+    end 
+end
+
+[r,c]=size(rbc);  
+mat=rbc; 
+mol_rbc=zeros(L_,c); 
+sum_mat=sum(rbc); 
+
+%find the mol%time for each lipid group
+for k=1:length(unique_);
+    indx=find(groups==unique_(k)); 
+    mat_=mat(indx,:); 
+    mat_species=sum(mat_); 
+    for j=1:c
+        mol_rbc(k,j)=mat_species(1,j)/sum_mat(1,j); 
+    end 
+end
+
+[r,c]=size(uninfected);  
+mat=uninfected; 
+mol_uninfected=zeros(L_,c); 
+sum_mat=sum(uninfected); 
+
+%find the mol%time for each lipid group
+for k=1:length(unique_);
+    indx=find(groups==unique_(k)); 
+    mat_=mat(indx,:); 
+    mat_species=sum(mat_); 
+    for j=1:c
+        mol_uninfected(k,j)=mat_species(1,j)/sum_mat(1,j); 
+    end 
+end
+plot_mat=zeros(L_,24); 
+plot_std=NaN(L_,24); 
+for k=1:length(unique_); 
+    label=species(k,2); 
+    c=1; 
+    d=1;
+    for j=1:6
+        plot_mat(k,c)=mean(mol_uninfected(k,:))*100;
+        std_dev=std(mol_uninfected(k,:)); 
+        plot_std(k,c)=(std_dev/sqrt(3))*100; 
+        c=c+1;  
+        plot_mat(k,c)=mean(mol_rbc(k,d:d+8))*100; 
+        std_dev=std(mol_rbc(k,d:d+8)); 
+        plot_std(k,c)=(std_dev/sqrt(9))*100; 
+        c=c+1;
+        plot_mat(k,c)=mean(mol_parasite(k,d:d+8))*100; 
+        std_dev=std(mol_parasite(k,d:d+8)); 
+        plot_std(k,c)=(std_dev/sqrt(9))*100; 
+        c=c+2; 
+        d=d+9; 
+    end
+    bar_color=[-1 0 1 0 -1 0 1 0 -1 0 1 0 -1 0 1 0 -1 0 1 0 -1 0 1 0]; 
+    bh=bar(plot_mat(k,:), 1); 
+    applyhatch(gcf,'\-x.');
+    title(label); 
+    hold on
+    c=1; 
+%    for j=1:6
+        errorbar (plot_mat(k,:), plot_std(k,:), '.k', 'MarkerSize', 2);
+%         c=c+4; 
+%     end 
+    hold off 
+    k_str=num2str(k); 
+    ch=get(bh,'Children');  
+    set (ch,'CData',bar_color) ; 
+    colormap (cmap); 
+    %x_label={'C', 'R', 'P', [], 'C', 'R', 'P', [], 'C', 'R', 'P', [], 'C', 'R', 'P', [], 'C', 'R', 'P', [], 'C', 'R', 'P', []}; 
+    x_label= {[],'8',[],[],[],'16',[],[],[],'24',[],[],[],'32',[],[],[],'40',[],[],[],'48',[],[]}; 
+    set(gca, 'XTick', [1:24]); 
+    set (gca, 'XTickLabel',x_label); 
+    xlim([0 25]); 
+    ylabel('Mol % of Total Lipids Measured'); 
+    print (gcf, '-dpng', [k_str 'figure1_bar.png']); 
+    close all 
+end 
+
+end
+