R/CustomFXs_Classifiers.R

In eisascience/scRNASeqEisa:

#Classifiers from the Caret package are kept together in the associated .R file.

Garnett_Classification_Seurat <- function(SerObj, 
                                          marker_file_path = "./data/Garnett/pbmc_classification.txt", 
                                          reutrnMonObj=F, returnTrainedClassifier=T){ 
  library(Seurat)
  library(ggplot2)
  library(cowplot)
  library(RColorBrewer)
  library(monocle)
  library(garnett)
  library(org.Hs.eg.db)
  
  tempStorageLS <- list()

  tempStorageLS$MonComboObj <- importCDS(SerObj, import_all = TRUE)
  
  
  tempStorageLS$MonComboObj <- estimateSizeFactors(tempStorageLS$MonComboObj)
  
  head(pData(tempStorageLS$MonComboObj))
  
  
  
  marker_check <- check_markers(tempStorageLS$MonComboObj,
                                marker_file_path,
                                db=org.Hs.eg.db,
                                cds_gene_id_type = "SYMBOL",
                                marker_file_gene_id_type = "SYMBOL")
  
  tempStorageLS$Garnett_classifier <- train_cell_classifier(cds = tempStorageLS$MonComboObj,
                                                         marker_file = marker_file_path,
                                                         db=org.Hs.eg.db,
                                                         cds_gene_id_type = "SYMBOL",
                                                         num_unknown = 50,
                                                         marker_file_gene_id_type = "SYMBOL")
  
  
  
  tempStorageLS$MonComboObj <- classify_cells(tempStorageLS$MonComboObj, 
                                           tempStorageLS$Garnett_classifier,
                                           db = org.Hs.eg.db,
                                           cluster_extend = TRUE,
                                           cds_gene_id_type = "SYMBOL")
  tempStorageLS$return <- list()
  tempStorageLS$return$Meta.Data <- pData(tempStorageLS$MonComboObj)
  if(reutrnMonObj) tempStorageLS$return$MonObj <- tempStorageLS$MonComboObj else tempStorageLS$return$MonObj <- "notSaved"
  if(returnTrainedClassifier) tempStorageLS$return$Garnett_classifier <- tempStorageLS$Garnett_classifier else tempStorageLS$return$Garnett_classifier <- "notSaved"
  return(tempStorageLS$return)

}