Refactor MOFA analysis vignette using provgigapath WSI embedding

[Eabousam]

Hi Marcel @LiNk-NY,

The goal of the issue is to refactor the MOFA analysis so the functions are not ran in the vignette but within the package.

Current state,

1. getEmbeddingLayer() function loops through the selected slides and uses provGiga() to import the whole slide level data

2. preparelayer() and prepareclinical() clean up the embedding layer and clinical data in preparation to be inputted as a summarized experiment

3. make_embedding_se() created the summarised experiment to be used in the MultiAssayExperiment() for MOFA.

4. run_mofa_pipeline(), runs mofa and allows the user to specify model output, currently fixed to fast convergence mode to allow the vignette to run relatively quickly but can be modified to allow the user to specify with a warning message.