Different input modes
Depending on your data and preferences, you case use 4 types of inputs. Specifically, it depends whether (i) you have one or multiple slides, and (ii) if you prefer to concatenate your data or not.
Info
In all cases, the data structure is AnnData. We may support MuData in the future.
1. One slide mode
This case is the easiest one. You simply have one AnnData object corresponding to one slide.
You can follow the first section of the main usage tutorial.
2. Multiple slides, one AnnData object
If you have multiple slides with the same gene panel, you can concatenate them into one AnnData object. In that case, make sure you keep a column in adata.obs that denotes which cell corresponds to which slide.
Then, remind this column, and pass it to the two following Novae methods: compute_representations and fine_tune. The other functions don't need this argument.
Example
For instance, you can do:
3. Multiple slides, one AnnData object per slide
If you have multiple slides, you may prefer to keep one AnnData object for each slide. This is also convenient if you have different gene panels and can't concatenate your data.
That case is pretty easy, since most functions and methods of Novae also support a list of AnnData objects as inputs. Therefore, simply pass a list of AnnData object, as below:
4. Multiple slides, multiple slides per AnnData object
If you have multiple slides and multiple panels, an alternative to option 3 is to have one AnnData object per panel, and multiple slides inside each AnnData object. In that case, make sure you keep a column in adata.obs that denotes which cell corresponds to which slide.
Then, remind this column, and pass it to the two following Novae methods: compute_representations and fine_tune. The other functions don't need this argument.