create spatial object from nono-10x data

[cadyyuheng]

Hello,

I'm also trying to create a spatial Seurat from scratch. While your hints in #3595 are quite straightforward to me for the term image and coordinates. However, I still don't quite get what scale.factors are other than it is a separate object. As I look into scalefactors function, I noticed scalefactors is defined by spot, fiducial, hires, and lowres values. From the doc, I don't fully understand what those values mean and how I could generalize them for my own data and image. Would you mind elaborating a bit more? I really appreciate your help!

[mojaveazure]

Sorry for the late response. The scale factors serve as a link between the coordinates and the image data. There are four scaling factors that 10X provides, but we generally only use the lowres factor. If you're using your own, non-10X data, simply create a fake scalefactors object with scalefactors, making sure that you use the correct factor for lowres. If you coordinates match 1:1 with your image, then your lowres scale factor would be 1