Cell-cell communication of Visium data

[boyiguo1]

• [x] Acquire spot deconvoluted Visium data at single cell level
  • Tangram or cell2location
• [ ] Format the single cell level Visium data according to SpaTalk Requirement
• [ ] Run SpaTalk with each sample using the K=13 layer specific cell type
• [ ] Run through all the sample
• [ ] Create spot figure with layer colored scheme highlighting the communication style from one cell type to another
  • Similar to the example plot in SpaTalk (also included below) except that cortex layers are highlighted in the spot plot.

[boyiguo1]

To my best understanding, between Tangram and cell2location, only Tangram provides single-cell resolution Visium data, via "Spatially resolved xxx patterns"

[boyiguo1]

Scripts to prep Visium CCC data: 27f4ae7 Under Boyi's drive ~/CCC_Visium/, creates each folder for each sample. Within each sample folder, a sample specific spe object is created.

[boyiguo1]

De-prioritize this analysis