#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)
}
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