step2—archr官网教程

.libPaths()
.libPaths(c("G:/R_big_packages/",
            "D:/Win10 System/Documents/R/win-library/4.1",
            "C:/Program Files/R/R-4.1.0/library",
            #"G:/sihuo/tatc/renv/library/R-4.1/x86_64-w64-mingw32",
            #"C:/Users/yll/AppData/Local/Temp/RtmpK2FJvt/renv-system-library"
            ))


getwd()
setwd("G:/sihuo/tatc")

#接着step1

library(ArchR)
addArchRThreads(threads = 16) 
addArchRGenome("hg19")


## tutorial  1.6
library(ArchR)
#inputFiles <- getTutorialData("Hematopoiesis")
#inputFiles #指向fragment的路径
#addArchRGenome("hg19")
## Setting default genome to Hg19.
#addArchRThreads(threads = 16) 
## Setting default number of Parallel threads to 16.
getwd()

??ArchRProject

projHeme2=loadArchRProject(path ="G:/sihuo/tatc/Save-ProjHeme2/" )


getAvailableMatrices(projHeme2)
head(getReducedDims(projHeme2))
names(getReducedDims(projHeme2))
projHeme2@reducedDims %>%names()
projHeme2$Clusters %>%table()
#CellColData(projHeme2)
getCellColData(projHeme2) #这里类似于metadata


pal<-ArchR::paletteDiscrete(values = unique(projHeme2$Clusters))
pal

plotEmbedding(ArchRProj = projHeme2,
              embedding = "UMAP",
              colorBy = "CellColData",
              name = "Clusters",
              imputeWeights =getImputeWeights(projHeme2) )

#library(ArchR)
#library(GenomeInfoDb)
#GenomeInfoDb::seqnames(projHeme2)
plotTSSEnrichment(projHeme2)

plotGroups(projHeme2)

#8.2 Adding Pseudo-scRNA-seq profiles for each scATAC-seq cell

projHeme2@cellMetadata 
projHeme2@projectSummary
projHeme2
projHeme2@cellColData %>%colnames()
getAvailableMatrices(projHeme2)
projHeme2@sampleMetadata

seRNA <- readRDS("./scRNA-Hematopoiesis-Granja-2019.rds")
seRNA
dim(seRNA)


#~5 minutes
is.installed <- "restfulr" %in% installed.packages()[, "Package"]
is.installed
#library(S4Vectors)
projHeme3 <- addGeneIntegrationMatrix(
  ArchRProj = projHeme2, 
  useMatrix = "GeneScoreMatrix",
  matrixName = "GeneIntegrationMatrix",
  reducedDims = "IterativeLSI",
  seRNA = seRNA,
  addToArrow = TRUE,
  force= TRUE,
  groupList = groupList,
  groupRNA = "BioClassification",
  nameCell = "predictedCell",
  nameGroup = "predictedGroup",
  nameScore = "predictedScore"
)
#Error in SimpleList(.) : could not find function "SimpleList"
#总是有报错，重新安装下



projHeme3=projHeme2
confusionMatrix(projHeme3$Clusters, projHeme3$predictedGroup)