Common and specific patterns between mouse brain anterior and posterior regions

Load the library and the data

library(SpaGene)
library(SeuratData)
library(Seurat)

brain1 <- LoadData("stxBrain", type = "anterior1")
brain2 <- LoadData("stxBrain", type = "posterior1")

count1<-GetAssayData(brain1,slot="counts")
count2<-GetAssayData(brain2,slot="counts")

 
location1<-GetTissueCoordinates(brain1)
location2<-GetTissueCoordinates(brain2)

Find spatially variable genes and patterns in two samples

spa1<-SpaGene(count1,location1)
spa2<-SpaGene(count2,location2)
 
pattern<-FindPattern_Multi(list(spa1,spa2),nPattern=25)

Plot common and specific patterns between two samples

locationlist<-list(location1[,2:1],location2[,2:1])
patternnum<-nrow(pattern$pattern)
for (i in 1:10) {
   cat(paste0("pattern ",i,"\n"))

   print(PlotPattern_Multi(pattern,locationlist,pt.size=1,patternid=i,max.cutoff =0.95))
}

## pattern 1

## pattern 2

## pattern 3

## pattern 4

## pattern 5

## pattern 6

## pattern 7

## pattern 8

## pattern 9

## pattern 10