library(batchelor)

library(scater)

library(BiocParallel)

library(BiocSingular)

adtf <- "../../Newcastle/combined_dec_ADT_SCE.RDS"

adt <- readRDS(adtf)

# There are some samples with no antibody signal, cool

rmSamples <- c("MH8919226","MH8919227","MH8919228","MH8919229","MH8919230","MH8919231","MH8919232","MH8919233")

# removing doublets identified by Mike and Kelvin

mk <- read.table("../data/doublets/Tcell_doublets.tsv",header=FALSE,sep="\t",stringsAsFactors=FALSE)

kl <- read.csv("../data/doublets/Karsten_doublets.csv",stringsAsFactors=FALSE)

dbls <- c(kl$doublets[kl$doublets!=""], mk$V1)

rmBcs <- colnames(adt)[adt$initial_clustering=="Doublet" | adt$sample_id %in% rmSamples]

rmBcs <- c(rmBcs,dbls)

adt <- adt[,!colnames(adt) %in% rmBcs]

set.seed(42)

adt1 <- adt[,adt$Site=="Cambridge"]

adt2 <- adt[,adt$Site=="Ncl"]

adt3 <- adt[,adt$Site=="Sanger"]

param <- MulticoreParam(workers=4)

print("Starting MNN")

set.seed(300)

mnncor <- batchelor::fastMNN(adt2,adt1,adt3,

             BPPARAM=param, # commented this out for singularity

             k=20,

             d=50,

             merge.order=c(1,2,3),

             BSPARAM=IrlbaParam(deferred=TRUE),

             assay.type="counts",

             #                      BNPARAM=AnnoyParam(),

             cos.norm=TRUE, # prob necesarry

             correct.all=TRUE)

print("Done MNN")

m.cor <- assay(mnncor,"reconstructed")

m.cor <- m.cor[,colnames(adt)]

assay(adt,"reconstructed") <- m.cor

saveRDS(adt,"../data/combined_dec_ADT_MNNcorrected.RDS")