How to plot a heatmap image using PCA loadings?

I need some guidance to plot or reconstruct a heatmap image as the attached image used PCA loading.

Answer 1

[Vandit]

Hi,

To plot or reconstruct a HeatMap image using PCA loadings, you can follow these general steps:

1. Use the 'pca()' function in MATLAB to perform PCA on your dataset and then determine the number of principal components you want to use for the reconstruction.
2. Determine the number of principal components you want to use for the reconstruction.
3. If your data was originally in a matrix or image format, reshape the reconstructed data back into the original shape and then use the 'imagesc()' function in MATLAB to plot the reconstructed heatmap image.

Here's an example code snippet that demonstrates these steps:

%Note:You should replace data with your actual data matrix or image. Adjust the numComponents variable to select the desired number of principal components for reconstruction


% Perform PCA on your data
pcaObj = pca(data);

% Select the desired number of principal components
numComponents = 10;
selectedComponents = pcaObj.coeff(:, 1:numComponents);

% Compute the scores for the selected principal components
scores = data * selectedComponents;

% Reconstruct the data
reconstructedData = scores * selectedComponents';

% Reshape the reconstructed data
reconstructedData = reshape(reconstructedData', size(data, 2), size(data, 1));

% Plot the heatmap
figure;
imagesc(reconstructedData);
colorbar;

To know more about 'pca' and 'imagesc' function, refer to the link below:

Principal component analysis of raw data - MATLAB pca (mathworks.com)

Display image with scaled colors - MATLAB imagesc (mathworks.com)

Hope this helps.

Thankyou