Your interpretation of the function outputs being transposes of each other is correct.
From the confusionmat documentation:
- C(i,j) is a count of observations known to be in group i but predicted to be in group j.
From the plotconfusion, documentation:
- On the confusion matrix plot, the rows correspond to the predicted class (Output Class), and the columns show the true class (Target Class).
So they are in fact transposes of each other.
I would use one or the other for consistency, depending on what you are doing. If you need to compare the, transpose one to the other, and be certain to note what the rows and columns represent.
