Patrick CN Martin comments

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                                            Patrick CN Martin

Inserting my own log normed PCA data

Hi, Replacing the PCA embedding with your own data is not possible in vesalius as this a core feature of the package. You will have to use the normalization offered...

Inserting my own log normed PCA data

In the current version there is no work around. The embedding and the way we use them is a core functionality of the package. Could you explain why this is...

Inserting my own log normed PCA data

I will leave this issue open and tag it as a feature request. As I said above, I will have a look into it for the next version. If anyone...

Inserting my own log normed PCA data

Understood. It will not change how the method works but it would require some changes to the core code that would need to be thoroughly tested to ensure that everything...

Inserting my own log normed PCA data

The code you will need to modify is in https://github.com/patrickCNMartin/Vesalius/blob/main/R/PCA_to_RGB.R I suspect you would be better off modifying the `rgbUMAP` function. Please note that once the new version is fully...

Inserting my own log normed PCA data

Good to know. I assume that this should do what you expect it to do as long as the `RunUMAP` function gets the correct reduction argument (`reduction.use = "pca"`. )...

Inserting my own log normed PCA data

In this case, I would advise you to build and install from source. You should have a local copy of the source code where you make your changes. To do...