add several scripts

STOMACH_ANALYSIS/Abundance_TMP.m

+% Abundance_individual_spceis calculates the abundance (occurance, RRA,
+% etc) for each spcies ('ALCES', 'COMP', 'COMBINED', 'CURVI', 'NUM',
+% 'TSHO', 'PET')
+%
+% Copyright (C) Rahma Amen 2021 Potsdam University
+
+tic
+clear
+close all
+addpath(genpath('~/Matlab_Functions/'))
+
+%% ============================== INPUTS =============================== %%
+
+% Folders
+KRAKEN_REPORT = '/home/mohamed/work/RAHMA/KRAKEN_REPORTS/';
+ABUNDANCE_DIR = '/home/mohamed/work/RAHMA/ABUNDANCE/';
+PLOT_DIR = '/home/mohamed/work/RAHMA/ABUNDANCE/PLOTS/';
+dir_pavian = '/home/mohamed/work/RAHMA/tmp/'; % folder of pavian csv files of top 100 taxa (C, O, F, G, S)
+
+% Settings
+TaxaRankName = 'Species';  % 'Class' or 'Order' or 'Family' or 'Genus' or 'Species'
+l_write_Abundance = 1;     % Write the abundance text file 
+l_clean_Abundance = 1;     % clean the abundance output folder
+l_individual      = 0;     % Plot the figures for individual level
+l_plot_pooled     = 1;     % Plot the figures for pooled level
+l_figsave = 1;             % save the figures
+l_num = 0;                 % include c. num in choosing the common taxa
+
+%% =================== T A X A  S E T T I N G S ======================== %%
+
+switch TaxaRankName
+    case 'Class'
+        TaxaRank = 'C';
+        nTaxa = 10;
+        
+    case 'Order'
+        TaxaRank = 'O';
+        nTaxa = 15;
+        
+    case 'Family'
+        TaxaRank = 'F';
+        nTaxa = 15;
+        
+    case 'Genus'
+        TaxaRank = 'G';
+        nTaxa = 15;
+        
+    case 'Species'
+        TaxaRank = 'S';
+        nTaxa = 15;
+        
+    otherwise
+        error('Not implemented yet.')
+end
+
+if l_individual
+    CASES = {'ALCES','COMP','COMBINED','CURVI','NUM','TSHO','PET'};
+else
+    CASES = {'COMBINED'};
+end
+
+Food_Taxa_list = find_commen_taxa(dir_pavian,TaxaRank,nTaxa,l_num);
+Food_Taxa_list = replace(Food_Taxa_list, char(160), char(32)); % This is very important to convert space with 160 char to 32 to compare spcies
+
+% Check that l_clean_Abundance is set intentionaly and clean accordingly
+if l_clean_Abundance
+    answer = questdlg('Would you like to delet Abundance folder?', ...
+        'Abundance Folder', ...
+        'Yes','No thank you','No thank you');
+    % Handle response
+    switch answer
+        case 'Yes'
+            cmd = ['rm -r ' ABUNDANCE_DIR '/*']; system(cmd);
+        case 'No thank you'
+            disp('OK. l_clean_Abundance is set to False')
+    end
+    
+end
+% Create Abundance folder
+if l_write_Abundance
+    if ~exist(ABUNDANCE_DIR, 'dir')
+        cmd = ['mkdir ' ABUNDANCE_DIR]; system(cmd);
+    end
+end
+
+%% Analysis
+
+% loop for each species and the pooled cases
+for i_case = 1:length(CASES)
+    
+    % Create sub-folder for each species
+    DIR = [KRAKEN_REPORT CASES{i_case} '/'];
+    DIR_OUT = [ABUNDANCE_DIR CASES{i_case} '/'];
+    if l_write_Abundance
+        if ~exist(DIR_OUT, 'dir')
+            cmd = ['mkdir ' DIR_OUT]; system(cmd);
+        end
+    end
+
+    REPORTS = dir([DIR '*_report']);
+    ABUNDANCE = zeros(length(REPORTS),length(Food_Taxa_list));
+
+    % Initiate the species of the pooled cases
+    if strcmp(CASES{i_case},'COMBINED')
+        SPECIS = strings(1,length(REPORTS));
+        % Note: SPECIS_NAME is not used because the text is not visiable
+        % below the figure. We decided to add it manually using Inkscape
+        SPECIS_NAME = strings(1,length(REPORTS)); 
+    end
+    
+    % loop for each KRAKEN report
+    for i_report = 1:length(REPORTS)
+        T = readtable( [DIR REPORTS(i_report).name]);
+        
+        disp(['Processing the case: ' REPORTS(i_report).name])
+        
+        % Define the species of the pooled cases
+        if strcmp(CASES{i_case},'COMBINED')
+            SPECIS(i_report)=erase(REPORTS(i_report).name,"_COMBINED_report");
+        end
+        
+        % Open abundance report
+        if l_write_Abundance
+            if strcmp(CASES{i_case},'COMBINED')
+                fname = [DIR_OUT SPECIS(i_report) '_' TaxaRankName];
+            else
+                fname = [DIR_OUT erase(REPORTS(i_report).name,"report") TaxaRankName];
+            end
+            fileID = fopen(join(fname,""),'w'); % join is used here to convert to text
+        end
+        
+        % loop for each food taxa
+        for i_food = 1:length(Food_Taxa_list)
+            n_class = 0;
+            
+            % loop for each line in KRAKEN report
+            for i_line = 1:length(T.Var1)
+                if strcmp(T.Var4(i_line),TaxaRank)              && ...
+                   strcmp(T.Var6{i_line},Food_Taxa_list{i_food})
+                    n_class = T.Var2(i_line);
+                    break
+                end
+            end
+            
+            % fill CASSES array
+            ABUNDANCE(i_report,i_food) = n_class;
+            if l_write_Abundance
+                fprintf(fileID,'%-14s %-12d\n',Food_Taxa_list{i_food}, ...
+                                               ABUNDANCE(i_report,i_food));
+            end
+        end
+    end
+    
+    % Calculate 
+    COUNT = ABUNDANCE;
+    COUNT(ABUNDANCE > 0) = 1;
+    COUNT_WEIGHT = COUNT./sum(COUNT,2)*100;
+    RRA = ABUNDANCE./sum(ABUNDANCE,2)*100;
+    
+    switch CASES{i_case}
+        case 'ALCES'
+            ABUNDANCE_ALCES = ABUNDANCE;
+            COUNT_ALCES = COUNT;
+            COUNT_WEIGHT_ALCES = COUNT_WEIGHT;
+            RRA_ALCES = RRA;
+        case 'COMP'
+            ABUNDANCE_COMP = ABUNDANCE;
+            COUNT_COMP = COUNT;
+            COUNT_WEIGHT_COMP = COUNT_WEIGHT;
+            RRA_COMP = RRA;
+        case 'COMBINED'
+            ABUNDANCE_COMBINED = ABUNDANCE;
+            COUNT_COMBINED = COUNT;
+            COUNT_WEIGHT_COMBINED = COUNT_WEIGHT;
+            RRA_COMBINED = RRA;
+        case 'CURVI'
+            ABUNDANCE_CURVI = ABUNDANCE;
+            COUNT_CURVI = COUNT;
+            COUNT_WEIGHT_CURVI = COUNT_WEIGHT;
+            RRA_CURVI = RRA;
+        case 'NUM'
+            ABUNDANCE_NUM = ABUNDANCE;
+            COUNT_NUM = COUNT;
+            COUNT_WEIGHT_NUM = COUNT_WEIGHT;
+            RRA_NUM = RRA;
+        case 'PET'
+            ABUNDANCE_PET = ABUNDANCE;
+            COUNT_PET = COUNT;
+            COUNT_WEIGHT_PET = COUNT_WEIGHT;
+            RRA_PET = RRA;
+        case 'TSHO'
+            ABUNDANCE_TSHO = ABUNDANCE;
+            COUNT_TSHO = COUNT;
+            COUNT_WEIGHT_TSHO = COUNT_WEIGHT;
+            RRA_TSHO = RRA;
+    end
+
+end
+
+%% Plot figure
+
+if ~exist(PLOT_DIR, 'dir')
+    cmd = ['mkdir ' PLOT_DIR]; system(cmd);
+end
+
+for i_case = 1:length(CASES)
+    
+    if strcmp(CASES{i_case},'COMBINED')
+        continue
+    end
+    
+    switch CASES{i_case}
+        case 'ALCES'
+            ABUNDANCE = ABUNDANCE_ALCES;
+            COUNT = COUNT_ALCES;
+            COUNT_WEIGHT = COUNT_WEIGHT_ALCES;
+            RRA = RRA_ALCES;
+            for i_specis = 1:length(SPECIS)
+                if strcmp(SPECIS{i_specis},'ALCES')
+                    i_sp = i_specis;
+                    SPECIS_NAME{i_sp}='C. alces';
+                    break
+                end
+            end
+            
+        case 'COMP'
+            ABUNDANCE = ABUNDANCE_COMP;
+            COUNT = COUNT_COMP;
+            COUNT_WEIGHT = COUNT_WEIGHT_COMP;
+            RRA = RRA_COMP;
+            for i_specis = 1:length(SPECIS)
+                if strcmp(SPECIS{i_specis},'COMP')
+                    i_sp = i_specis;
+                    SPECIS_NAME{i_sp}='C. compressirostris';
+                    break
+                end
+            end
+            
+        case 'CURVI'
+            ABUNDANCE = ABUNDANCE_CURVI;
+            COUNT = COUNT_CURVI;
+            COUNT_WEIGHT = COUNT_WEIGHT_CURVI;
+            RRA = RRA_CURVI;
+            for i_specis = 1:length(SPECIS)
+                if strcmp(SPECIS{i_specis},'CURVI')
+                    i_sp = i_specis;
+                    SPECIS_NAME{i_sp}='C. curvirostris';
+                    break
+                end
+            end
+            
+        case 'NUM'
+            ABUNDANCE = ABUNDANCE_NUM;
+            COUNT = COUNT_NUM;
+            COUNT_WEIGHT = COUNT_WEIGHT_NUM;
+            RRA = RRA_NUM;
+            for i_specis = 1:length(SPECIS)
+                if strcmp(SPECIS{i_specis},'NUM')
+                    i_sp = i_specis;
+                    SPECIS_NAME{i_sp}='C. numenius';
+                    break
+                end
+            end
+            
+        case 'PET'
+            ABUNDANCE = ABUNDANCE_PET;
+            COUNT = COUNT_PET;
+            COUNT_WEIGHT = COUNT_WEIGHT_PET;
+            RRA = RRA_PET;
+            for i_specis = 1:length(SPECIS)
+                if strcmp(SPECIS{i_specis},'PET')
+                    i_sp = i_specis;
+                    SPECIS_NAME{i_sp}='G. petersii';
+                    break
+                end
+            end
+            
+        case 'TSHO'
+            ABUNDANCE = ABUNDANCE_TSHO;
+            COUNT = COUNT_TSHO;
+            COUNT_WEIGHT = COUNT_WEIGHT_TSHO;
+            RRA = RRA_TSHO;
+            for i_specis = 1:length(SPECIS)
+                if strcmp(SPECIS{i_specis},'TSHO')
+                    i_sp = i_specis;
+                    SPECIS_NAME{i_sp}='C. tshokwe';
+                    break
+                end
+            end
+    end
+    
+    % individual plots
+    if l_individual
+        
+        fname = [PLOT_DIR CASES{i_case} '_' TaxaRankName '_COUNT.pdf'];
+        COUNT(end+1,:) = COUNT_COMBINED(i_sp,:);
+        plot_abundance(COUNT,fname,'Count',size(COUNT_COMBINED,2),      ...
+                       Food_Taxa_list,0,0,l_figsave)
+        
+        fname = [PLOT_DIR CASES{i_case} '_' TaxaRankName '_COUNT_WEIGHT.pdf'];
+        COUNT_WEIGHT(end+1,:) = COUNT_WEIGHT_COMBINED(i_sp,:);
+        plot_abundance(COUNT_WEIGHT,fname,'Occurrence, %',100,          ...
+                       Food_Taxa_list,0,0,l_figsave)
+        
+        fname = [PLOT_DIR CASES{i_case} '_' TaxaRankName '_RRA.pdf'];
+        RRA(end+1,:) = RRA_COMBINED(i_sp,:);
+        plot_abundance(RRA,fname,'Relative read abundance, %',100,      ...
+                       Food_Taxa_list,0,0,l_figsave)
+    end
+    
+end
+%%
+% Pooled plots
+close all
+if l_plot_pooled
+    fname = [PLOT_DIR 'COMBINED' '_' TaxaRankName '_RRA.pdf'];
+    plot_abundance(RRA_COMBINED,fname,'Relative read abundance, %',100, ...
+                   Food_Taxa_list,0,1,l_figsave)
+    fname = [PLOT_DIR 'COMBINED' '_' TaxaRankName '_RRA_Legend.pdf'];
+    plot_abundance(RRA_COMBINED,fname,'Relative read abundance, %',100, ...
+                   Food_Taxa_list,1,1,l_figsave)
+end
+
+toc
+
+function plot_abundance(ab,fn,ylbl,ylm,lgd,l_lgd,l_p,l_save)
+
+fz = 26; fzlgnd = 12; lw = 1.5;
+h = figure('units','normalized','outerposition',[0 0 1 1]);
+bh = bar(ab,'stacked');
+
+% Change the colors of the stacked bars
+set(bh, 'FaceColor', 'Flat')
+% clrs = mat2cell(distinguishable_colors(numel(bh)),ones(numel(bh),1),3); % here we need the external function distinguishable_colors, otherwise use jet
+% clrs = mat2cell(linspecer(numel(bh)),ones(numel(bh),1),3); % here we need the external function distinguishable_colors, otherwise use jet
+clrs = mat2cell(cbrewer('div','Spectral',numel(bh),'PCHIP'),ones(numel(bh),1),3); % here we need the external function distinguishable_colors, otherwise use jet
+set(bh, {'CData'}, flip(clrs))
+
+% Remove x axis
+set(gca,'XTick',[])
+set(gca,'XColor','white')
+bh(1).BaseLine.Visible = 'off';
+box off
+
+% White figure
+set(gcf,'InvertHardCopy','off','Color','white');
+ylim([0 ylm])
+
+% Add * for combined bar
+if l_p < 1
+    text(size(ab,1),0,'*','HorizontalAlignment','center', ...
+        'VerticalAlignment','top','FontSize',fz);
+end
+
+% adjust axis
+set(gca,'FontSize',fz); set(gca,'linewidth',lw,'FontName','Times')
+if l_p < 1
+    xlabel('Samples','FontName','Times','FontSize',fz,'Color','black')
+end
+ylabel(ylbl,'FontName','Times','FontSize',fz)
+
+% legend
+if l_lgd
+    legend(lgd,'Location','northeastoutside','FontSize',fzlgnd)
+end
+
+%save file
+if l_save
+    export_fig(h,fn,'-m2')
+    close(h)
+end
+
+end
+
+function cns = find_commen_taxa(dir_pavian,taxa,ntaxa,lnum)
+
+if lnum
+    cases = {'ALCES','COMP','CURVI','NUM','TSHO','PET'};
+else
+    cases = {'ALCES','COMP','CURVI','TSHO','PET'};
+end
+
+for i = 1:length(cases)
+    f = [dir_pavian cases{i} '-results-211107_' taxa '.csv'];
+    Table = readtable(f);
+    n = min(ntaxa, length(Table.Name));
+    TaxaCases(i,1:n) = Table.Name(1:n);
+    TaxaNumbr(i,1:n) = Table.CladeReads(1:n);
+end
+
+c = unique(TaxaCases);
+c(cellfun('isempty',c)) = [];
+cn = zeros(length(c),2);
+
+for i = 1:length(cases)
+    for j = 1:length(c)
+        cn(j,2) = j;
+        for k = 1:ntaxa
+            if strcmp(c{j},TaxaCases{i,k})
+                cn(j,1) = cn(j,1) + str2double(TaxaNumbr(i,k));
+            end
+        end
+    end
+end
+
+b = sortrows(cn,1,'descend');
+
+for i = 1:length(c)
+    cns{i} = c{b(i,2)};
+end
+
+end

STOMACH_ANALYSIS/Abundance_all_species.m

+% Abundance_all_spceis calculates the abundance (occurance, RRA, etc) for
+% all the spcies ('ALCES','COMP','COMBINED','CURVI','NUM','TSHO','PET')
+%
+% Copyright (C) Rahma Amen 2021 Potsdam University
+
+tic
+clear
+close all
+addpath(genpath('~/Matlab_Functions/'))
+
+%% ============================== INPUTS =============================== %%
+
+% Folders
+KRAKEN_REPORT = '/home/mohamed/work/RAHMA/KRAKEN_REPORTS/';
+ABUNDANCE_DIR = '/home/mohamed/work/RAHMA/ABUNDANCE/';
+PLOT_DIR = '/home/mohamed/work/RAHMA/ABUNDANCE/PLOTS/';
+PAVIAN_DIR = '/home/mohamed/work/RAHMA/PAVIAN_CSV/'; % folder of pavian csv files of top 100 taxa (C, O, F, G, S)
+
+% Settings
+TaxaRankName = 'Class';    % 'Class' or 'Order' or 'Family' or 'Genus' or 'Species'
+l_write_Abundance = 1;     % Write the abundance text file 
+l_clean_Abundance = 1;     % clean the abundance output folder
+l_figsave = 1;             % save the figures
+l_numenius = 0;            % include c. num in choosing the common taxa
+
+%% =================== T A X A  S E T T I N G S ======================== %%
+
+switch TaxaRankName
+    case 'Class'
+        TaxaRank = 'C';
+        nTaxa = 10;
+        
+    case 'Order'
+        TaxaRank = 'O';
+        nTaxa = 15;
+        
+    case 'Family'
+        TaxaRank = 'F';
+        nTaxa = 15;
+        
+    case 'Genus'
+        TaxaRank = 'G';
+        nTaxa = 15;
+        
+    case 'Species'
+        TaxaRank = 'S';
+        nTaxa = 15;
+        
+    otherwise
+        error('Not implemented yet.')
+end
+
+CASES = {'COMBINED'};
+
+Food_Taxa_list = find_commen_taxa(PAVIAN_DIR,TaxaRank,nTaxa,l_numenius);
+Food_Taxa_list = replace(Food_Taxa_list, char(160), char(32)); % This is very important to convert space with 160 char to 32 to compare spcies
+
+% Check that l_clean_Abundance is set intentionaly and clean accordingly
+if l_clean_Abundance
+    answer = questdlg('Would you like to delet Abundance folder?', ...
+        'Abundance Folder', ...
+        'Yes','No thank you','No thank you');
+    % Handle response
+    switch answer
+        case 'Yes'
+            cmd = ['rm -r ' ABUNDANCE_DIR '/COMBINED']; system(cmd);
+        case 'No thank you'
+            disp('OK. l_clean_Abundance is set to False')
+    end
+    
+end
+% Create Abundance folder
+if l_write_Abundance
+    if ~exist(ABUNDANCE_DIR, 'dir')
+        cmd = ['mkdir ' ABUNDANCE_DIR]; system(cmd);
+    end
+end
+
+%% Analysis
+
+% loop for each species and the pooled cases
+% for i_case = 1:length(CASES)
+    
+% Create sub-folder for each species
+DIR = [KRAKEN_REPORT CASES{1} '/'];
+DIR_OUT = [ABUNDANCE_DIR CASES{1} '/'];
+if l_write_Abundance
+    if ~exist(DIR_OUT, 'dir')
+        cmd = ['mkdir ' DIR_OUT]; system(cmd);
+    end
+end
+
+REPORTS = dir([DIR '*_report']);
+ABUNDANCE = zeros(length(REPORTS),length(Food_Taxa_list));
+
+% Initiate the species of the pooled cases
+SPECIS = strings(1,length(REPORTS));
+% Note: SPECIS_NAME is not used because the text is not visiable
+% below the figure. We decided to add it manually using Inkscape
+SPECIS_NAME = strings(1,length(REPORTS));
+    
+% loop for each KRAKEN report
+for i_report = 1:length(REPORTS)
+    T = readtable( [DIR REPORTS(i_report).name]);
+    
+    disp(['Processing the case: ' REPORTS(i_report).name])
+    
+    SPECIS(i_report)=erase(REPORTS(i_report).name,"_COMBINED_report");
+    
+    % Open abundance report
+    if l_write_Abundance
+        fname = [DIR_OUT SPECIS(i_report) '_' TaxaRankName];
+        fileID = fopen(join(fname,""),'w'); % join is used here to convert to text
+    end
+        
+    % Combine case: loop for each food taxa
+    for i_food = 1:length(Food_Taxa_list)
+        n_class = 0;
+        
+        % loop for each line in KRAKEN report
+        for i_line = 1:length(T.Var1)
+            if strcmp(T.Var4(i_line),TaxaRank)              && ...
+                    strcmp(T.Var6{i_line},Food_Taxa_list{i_food})
+                n_class = T.Var2(i_line);
+                break
+            end
+        end
+        
+        % fill CASSES array
+        ABUNDANCE(i_report,i_food) = n_class;
+        if l_write_Abundance
+            fprintf(fileID,'%-14s %-12d\n',Food_Taxa_list{i_food}, ...
+                ABUNDANCE(i_report,i_food));
+        end
+    end
+    
+end
+    
+% Calculate count, count_weight, RRA
+COUNT_COMBINED = ABUNDANCE;
+COUNT_COMBINED(ABUNDANCE > 0) = 1;
+COUNT_WEIGHT_COMBINED = COUNT_COMBINED./sum(COUNT_COMBINED,2)*100;
+RRA_COMBINED = ABUNDANCE./sum(ABUNDANCE,2)*100;
+
+%% Plot figure
+
+if ~exist(PLOT_DIR, 'dir')
+    cmd = ['mkdir ' PLOT_DIR]; system(cmd);
+end
+
+%% =========================  P L O T S  ================================%%
+
+fname = [PLOT_DIR 'COMBINED' '_' TaxaRankName '_RRA.pdf'];
+plot_abundance(RRA_COMBINED,fname,'Relative read abundance, %',100, ...
+    Food_Taxa_list,0,1,l_figsave)
+fname = [PLOT_DIR 'COMBINED' '_' TaxaRankName '_RRA_Legend.pdf'];
+plot_abundance(RRA_COMBINED,fname,'Relative read abundance, %',100, ...
+    Food_Taxa_list,1,1,l_figsave)
+
+toc
+
+function plot_abundance(ab,fn,ylbl,ylm,lgd,l_lgd,l_p,l_save)
+
+fz = 26; fzlgnd = 12; lw = 1.5;
+h = figure('units','normalized','outerposition',[0 0 1 1]);
+bh = bar(ab,'stacked');
+
+% Change the colors of the stacked bars
+set(bh, 'FaceColor', 'Flat')
+% clrs = mat2cell(distinguishable_colors(numel(bh)),ones(numel(bh),1),3); % here we need the external function distinguishable_colors, otherwise use jet
+% clrs = mat2cell(linspecer(numel(bh)),ones(numel(bh),1),3); % here we need the external function distinguishable_colors, otherwise use jet
+clrs = mat2cell(cbrewer('div','Spectral',numel(bh),'PCHIP'),ones(numel(bh),1),3); % here we need the external function distinguishable_colors, otherwise use jet
+set(bh, {'CData'}, flip(clrs))
+
+% Remove x axis
+set(gca,'XTick',[])
+set(gca,'XColor','white')
+bh(1).BaseLine.Visible = 'off';
+box off
+
+% White figure
+set(gcf,'InvertHardCopy','off','Color','white');
+ylim([0 ylm])
+
+% Add * for combined bar
+if l_p < 1
+    text(size(ab,1),0,'*','HorizontalAlignment','center', ...
+        'VerticalAlignment','top','FontSize',fz);
+end