% QCB W12: Intro to MATLAB
% W12_Day2_student_updated_v1
% -----------------------------------
% Day 2 - Improved Examples and Explanations
%%
% Define variables
mynumber = 3.34;
myvect = [1; 2; 3];
myarray = [1, 2, 3; 4, 5, 6];
%%
% Demonstrate array/matrix functions
disp('Array size and matrix operations examples:');
size(myarray) % Display size of the matrix
myrange = 1:2:10; % Generate a range with step size 2
disp('Range:');
disp(myrange);
%%
% Matrix element-wise operations
result = [1, 2, 3] .^ 2; % Square each element
disp('Element-wise operations:');
disp(result);
%%
% Demonstrate functions
sinValues = sin(pi * [1, 2, 3]); % Compute sine values
disp('Sine values:');
disp(sinValues);
%%
% Access matrix elements
a = [1, 2; 3, 4];
disp('Matrix element a(1,2):');
disp(a(1, 2));
%%
% Nested for loops for matrix traversal
for ii = 1:size(a, 1)
    for jj = 1:size(a, 2)
        fprintf('a(%d,%d) = %.2f\n', ii, jj, a(ii, jj));
    end
end
%%
% Writing to a formatted text file
fileName = 'outputData.tab';
fileID = fopen(fileName, 'w');
for ii = 1:size(a, 1)
    fprintf(fileID, '%8.2f\t', a(ii, :));
    fprintf(fileID, '\n');
end
fclose(fileID);
%%
% Reading from a file
data = readtable('dataFile.txt'); % Example file read
disp('Data from file:');
disp(data);

% Note: Ensure 'dataFile.txt' exists in the current folder.
%%
% QCB W12: Intro to MATLAB
% W12_Day2_student_updated_v2
% -----------------------------------
% Recap of fundamental MATLAB concepts
%%
% Define variables and arrays
mynumber = 3.34;
myvect = [1; 2; 3];
myarray = [1, 2, 3; 4, 5, 6];
%%
% Display array size and operations
disp('Array size:');
disp(size(myarray));
%%
% Generating arrays: ones, zeros, eye, rand, randn
onesArray = ones(2, 3);
zerosArray = zeros(2, 3);
identityMatrix = eye(3);
randomArray = rand(2, 3);
normalRandomArray = randn(2, 3);
%%
% Generating ranges
range1 = 1:10;
range2 = 1:2:10;
disp('Generated Ranges:');
disp(range1);
disp(range2);
%%
% Element-wise operations
result1 = [1, 2, 3] .^ 2; % Element-wise squaring
result2 = [1, 2; 3, 4] ^ 2; % Matrix multiplication
disp('Element-wise operation results:');
disp(result1);
%%
% Functions and matrix operations
sinValues = sin(pi * [1, 2, 3]);
matrixSum = sum(myarray, 2); % Sum along rows
matrixMean = mean(myarray, 1); % Mean along columns
disp('Sine values:');
disp(sinValues);
%%
% Accessing elements and slices of a matrix
a = [1, 2; 3, 4];
disp('Matrix element a(1,2):');
disp(a(1, 2));
%%
% Nested for loops for matrix traversal
for ii = 1:size(a, 1)
    for jj = 1:size(a, 2)
        fprintf('a(%d,%d) = %.2f\n', ii, jj, a(ii, jj));
    end
end
%%
% Formatted output using fprintf
a = [1, 2, 3, 4; 11, 22, 33, 44];
for ii = 1:size(a, 1)
    for jj = 1:size(a, 2)
        fprintf('%10d %10d : %8.2f\n', ii, jj, a(ii, jj));
    end
end
%%
% Writing formatted data to a file
fileName = 'myfile2.tab';
fileID = fopen(fileName, 'w');
for ii = 1:size(a, 1)
    for jj = 1:size(a, 2)
        fprintf(fileID, '%8.2f\t', a(ii, jj));
    end
    fprintf(fileID, '\n');
end
fclose(fileID);
%%
% Reading files
% numData = importdata('edata/numfile.txt');
% numTable = readtable('edata/numfile.txt');
% mixData = readtable('edata/flist.txt');
%%
% Example plotting
series = readtable('series.txt');
disp('Series data loaded for plotting');

% QCB W12: Intro to MATLAB
% importfile_updated_v1
% -----------------------------------
function dataTable = importFile(filename, dataLines)
    % IMPORTFILE imports data from a specified text file into a table.
    % Inputs:
    % - filename: Path to the text file.
    % - dataLines: Row intervals for reading (default: [2, Inf]).
    
    % Set default dataLines if not provided
    if nargin < 2
        dataLines = [2, Inf];
    end
    
    % Configure import options
    opts = delimitedTextImportOptions("NumVariables", 3);
    opts.DataLines = dataLines;
    opts.Delimiter = "\t";
    opts.VariableNames = ["Var1", "Name", "Expression"];
    opts.SelectedVariableNames = ["Name", "Expression"];
    opts.VariableTypes = ["string", "string", "double"];
    opts.ExtraColumnsRule = "ignore";
    opts.EmptyLineRule = "read";
    opts = setvaropts(opts, ["Var1", "Name"], "WhitespaceRule", "preserve");
    opts = setvaropts(opts, ["Var1", "Name"], "EmptyFieldRule", "auto");
    
    % Attempt to read the table, with error handling
    try
        dataTable = readtable(filename, opts);
    catch ME
        error('Failed to read file: %s\nError: %s', filename, ME.message);
    end
end
%%
% QCB W12: Intro to MATLAB
% importfile_updated_v2
% -----------------------------------
function YBL005W = importFile(filename, dataLines)
    % IMPORTFILE Imports data from a text file into a MATLAB table.
    % YBL005W = IMPORTFILE(FILENAME) reads data from FILENAME with default row range [2, Inf].
    % YBL005W = IMPORTFILE(FILENAME, DATALINES) reads data from specified row intervals.
    %
    % Example: YBL005W = importFile("C:\path\to\your\file.txt", [2, Inf]);
    %
    % Auto-generated by MATLAB on 31-Oct-2024

    % Handle optional input
    if nargin < 2
        dataLines = [2, Inf];
    end

    % Set up the import options
    opts = delimitedTextImportOptions("NumVariables", 3);
    opts.DataLines = dataLines;
    opts.Delimiter = "\t";
    opts.VariableNames = ["Var1", "Name", "expr"];
    opts.SelectedVariableNames = ["Name", "expr"];
    opts.VariableTypes = ["string", "string", "double"];
    opts.ExtraColumnsRule = "ignore";
    opts.EmptyLineRule = "read";
    opts = setvaropts(opts, ["Var1", "Name"], "WhitespaceRule", "preserve");
    opts = setvaropts(opts, ["Var1", "Name"], "EmptyFieldRule", "auto");

    % Try reading the file
    try
        YBL005W = readtable(filename, opts);
    catch ME
        error('Error reading file %s: %s', filename, ME.message);
    end
end

% QCB W12: Intro to MATLAB
% merge_updated_v1
% -----------------------------------
function mergedData = mergeDataFiles(fileListPath)
    % MERGEDATAFILES imports and merges data from a list of text files.
    % Input:
    % - fileListPath: Path to the file containing the list of files to merge.
    
    % Read file list
    opts = delimitedTextImportOptions("NumVariables", 1, "DataLines", [2, Inf]);
    opts.Delimiter = ",";
    opts.VariableNames = "file";
    opts.VariableTypes = "string";
    opts.ExtraColumnsRule = "ignore";
    opts.EmptyLineRule = "read";
    opts = setvaropts(opts, "file", "WhitespaceRule", "preserve");
    opts = setvaropts(opts, "file", "EmptyFieldRule", "auto");
    
    try
        fileList = readtable(fileListPath, opts);
    catch ME
        error('Error reading file list: %s', ME.message);
    end
    
    % Initialize variables
    mergedData = table();
    labels = {};
    
    % Iterate through each file
    for ii = 1:height(fileList)
        fileName = fileList.file{ii};
        data = importFile(fileName);
        
        % Process data if it meets criteria
        expr = data.Expression;
        if mean(expr) > -1
            geneName = extractBefore(fileName, ".txt");
            mergedData = [mergedData, table(expr, 'VariableNames', {geneName})]; %#ok<AGROW>
            labels = [labels, {geneName}]; %#ok<AGROW>
        end
    end
    
    % Plot the data using the improved boxplot function
    createBoxPlot(mergedData{:,:}, labels);
end

%%
% QCB W12: Intro to MATLAB
% merge_updated_v2
% -----------------------------------
% Import data from a text file
% This script reads multiple text files specified in a list and merges them
% Auto-generated by MATLAB on 31-Oct-2024

% Set up the import options
opts = delimitedTextImportOptions("NumVariables", 1);
opts.DataLines = [2, Inf];
opts.Delimiter = ",";
opts.VariableNames = "file";
opts.VariableTypes = "string";
opts.ExtraColumnsRule = "ignore";
opts.EmptyLineRule = "read";
opts = setvaropts(opts, "file", "WhitespaceRule", "preserve");
opts = setvaropts(opts, "file", "EmptyFieldRule", "auto");

% Import the file list
try
    flist = readtable("C:\Users\lukasz\Desktop\W12\split\flist.txt", opts);
catch ME
    error('Error reading file list: %s', ME.message);
end

% Initialize variables
etab = table();
labels = {};

% Loop through each file in the list
for ii = 1:height(flist)
    fileName = flist.file{ii};
    series = importFile(fileName); % Use the updated import function
    expr = series.expr;

    % Process and merge data if mean(expr) > -1
    if mean(expr) > -1
        geneName = extractBefore(fileName, ".txt");
        etab = [etab, table(expr, 'VariableNames', {geneName})]; %#ok<AGROW>
        labels = [labels, {geneName}]; %#ok<AGROW>
        fprintf('%s %s\n', fileName, geneName); % Output for logging
    end
end

% Create box plot using the custom function
createBoxPlot(etab{:,:}, labels);

% QCB W12: Intro to MATLAB
% createboxplot_updated_v1
% -----------------------------------
function createBoxPlot(yData, xLabels)
    % CREATEBOXPLOT generates a box plot for the given data with labeled x-axis.
    % Inputs:
    % - yData: Data to be represented in the box chart (numeric array).
    % - xLabels: Labels for each data category (cell array of strings).
    
    % Check input validity
    if nargin < 2 || isempty(yData) || isempty(xLabels)
        error('Both yData and xLabels must be provided and non-empty.');
    end
    
    % Create figure
    figureHandle = figure('Name', 'Box Plot', 'NumberTitle', 'off');
    
    % Create axes and hold for multiple plots if necessary
    axesHandle = axes('Parent', figureHandle);
    hold(axesHandle, 'on');
    
    % Plot box chart
    boxchart(yData, 'BoxFaceColor', 'cyan');
    xticklabels(xLabels);
    
    % Set title and labels
    title('Box Plot of Given Data');
    xlabel('Categories');
    ylabel('Values');
    
    % Release the hold state
    hold(axesHandle, 'off');
end
%%
% QCB W12: Intro to MATLAB
% createboxplot_updated_v2
% -----------------------------------
function createBoxPlot(ydata1, xlabels)
    % CREATEBOXPLOT Generates a box plot for the provided data.
    % ydata1: Data to be represented in the boxchart (numeric array)
    % xlabels: Labels for the categories on the x-axis (cell array of strings)

    % Check for valid input arguments
    if nargin < 2 || isempty(ydata1) || isempty(xlabels)
        error('Both ydata1 and xlabels must be provided and cannot be empty.');
    end

    % Create figure
    figure1 = figure('Name', 'Box Plot', 'NumberTitle', 'off');

    % Create axes and hold
    axes1 = axes('Parent', figure1);
    hold(axes1, 'on');

    % Create boxchart
    boxchart(ydata1);
    xticklabels(xlabels);

    % Enhance plot with labels and title
    title('Box Chart Representation');
    xlabel('Categories');
    ylabel('Values');

    % Release the hold
    hold(axes1, 'off');
end