How to apply PCA for my dataset

Hi,

I am trying to apply pca on my dataset but I am not able to get bioplot. I just need bioplot for my data. Please help me. I am very new to Matlab.

I have attached by dataset

Thanks

Answer 1

[Taylor]

The Reduce Dimensionality Live Task is perfect for this. Select "show code" at the bottom of the task and from there you can modify the code to your needs.

[shagun]

Thankyou so much bit I am getting this error

Execution of script pca as a function is not supported:

[shagun]

thank you so much It works . I am extremely grateful

[shagun]

Also, I have a question of getting PC1 v/s PC2 but If i want PC1 V/S PC3, how can i get. Just two individual plot of pc1/pc2, pc1v/spc3.

Please let me know .

I will be extremely grateful

thanks

[Taylor]

The second output (scores) from pca will contain your PCA scores. Each column corresponds to a component, and the percentage of variance explained by that component is stored in the corresponding row of the output explained.

Your data also has a lot of NaNs, so I would recommend looking at this section of the documentation as well.

[shagun]

thanks, but how should i put variable name on my graph.

[Taylor]

You can use the legend, xlabel, and ylabel functions to label your plot.

Answer 2

[shagun]

Thank you, But i want my variable name on the graph like same as attached in screenshot.

Thanks

[Taylor]

You can use the VarLabels input to biplot.

[shagun]

I have tried but I am getting this error

load (Datagroup)
% Extract numeric variables from table
numericVars = varfun(@isnumeric,Datagroup,"output","uniform");
numericPredictorTable = Datagroup(:, numericVars);

% Convert table to matrix
numericPredictorMatrix = table2array(varfun(@double, numericPredictorTable));

% Principal Component Analysis
[coeffs, transformedData, ~, ~, explained] = pca(numericPredictorMatrix);

% Compute number of components from explained variance
enoughExplained = cumsum(explained)/sum(explained) >= 95/100;
numberOfComponentsToKeep = find(enoughExplained, 1);
disp("The number of components needed to explain at least 95% of the variance is "+ num2str(numberOfComponentsToKeep))

% Display results
figure
colorMap = colormap("lines");
barPlot = bar(explained);
hold on;
plot(cumsum(explained),"*-","Color",colorMap(3,:));
hold off;
barPlot(1).FaceColor = "flat";
barPlot(1).CData(1:numberOfComponentsToKeep,:) = repmat( ...
    colorMap(2,:),[numberOfComponentsToKeep 1]);
label = ["Selected components"; sprintf("Cumulative explained\nvariance")];
legend(label,"Location","best");
title("Scree Plot of Explained Variances")
xlabel("Principal component")
ylabel("Variance explained (%)")
clear barPlot colorMap label explained

figure
scatter(transformedData(:,1),transformedData(:,2), "Marker", ".");
title("Scatter Plot of Principal Components")
xlabel("Component 1")
ylabel("Component 2")
variableNames = {'TSSLV10', 'TSSLV20', 'TSSLV30', 'TSSLV40', 'TSSLV50', 'TSSLV60', 'TSSLV70', 'TSSLV80', 'TSSLV90', ...
                 'TPLV10', 'TPLV20', 'TPLV30', 'TPLV40', 'TPLV50', 'TPLV60', 'TPLV70', 'TPLV80', 'TPLV90', ...
                 'SRPLV10', 'SRPLV20', 'SRPLV30', 'SRPLV40', 'SRPLV50', 'SRPLV60', 'SRPLV70', 'SRPLV80', 'SRPLV90', ...
                 'RDep10', 'RDep20', 'RDep30', 'RDep40', 'RDep50', 'RDep60', 'RDep70', 'RDep80', 'RDep90', ...
                 'AI10', 'AI20', 'AI30', 'AI40', 'AI50', 'AI60', 'AI70', 'AI80', 'AI90', ...
                 'RD10', 'RD20', 'RD30', 'RD40', 'RD50', 'RD60', 'RD70', 'RD80', 'RD90', 'TRD', 'AI', 'RD', 'ADP (HR)'};
             
figure
biplot(coeffs(:,[1 2],'VarLabels', variableNames));
title("PCA Biplot")
xlabel("Component 1")
ylabel("Component 2")
clear coeffs enoughExplained explained numericPredictorMatrix numericPredictorTable varLabels
transformedData = transformedData(:,1:numberOfComponentsToKeep);
clear numberOfComponentsToKeep
transformedData = array2table(transformedData);
transformedData = [transformedData,Datagroup(:,~numericVars)];
clear numericVars

Unable to use a value of type cell as an index.

[shagun]

I am getting this error of Unable to use a value of type cell as an indexUnable to use a value of type cell as an index