03a_labelTransfer_sct_integrated_pilot.R

##################################################
## Project: Label Transfer Cell Types, SCT & Integration
## Date: 26.05.2020
## Author: Nathalie
##################################################

# setwd("/net/PE1/raid1/LAURA/SC_ANALYSIS/markerGeneDefinition")
# 
# library(scrattch.io, lib.loc="pkg_r")
# library(Seurat, lib.loc="pkg_r")
# library(dplyr)
# library(pryr, lib.loc="pkg_r")
# library(RColorBrewer)

setwd("~/Documents/PostmortemBrain/analysis/markerGeneDefinition")

library(Seurat)
library(dplyr)
library(pryr)
library(RColorBrewer)


### TRANSFER CELL TYPES FROM ALLAN BRAIN ATLAS ########################

data <- readRDS("pilot/data_object_sct_integrated.rds")
referenceAllan <- readRDS("allan_human/data_object_sct.rds")
#referenceAllan <- subset(referenceAllan, subclass_label!="Exclude")

# Find cell type transfer anchors
brain.anchors <- FindTransferAnchors(reference = referenceAllan,
                                     query = data,
                                     normalization.method = "SCT",
                                     dims = 1:30)

ref1 <- referenceAllan$subclass_label
ref2 <- referenceAllan$cluster_label
rm(referenceAllan)

# Transfer labels from the 20 subclasses
predictions_subclass <- TransferData(anchorset = brain.anchors,
                                     refdata = ref1)
predictions_subclass <- predictions_subclass$predicted.id
data <- AddMetaData(data,
                    metadata = predictions_subclass,
                    col.name = 'predictions_subclass')

# Transfer labels from the 141 clusters
predictions_cluster <- TransferData(anchorset = brain.anchors,
                                    refdata = ref2)
predictions_cluster <- predictions_cluster$predicted.id
data <- AddMetaData(data,
                    metadata = predictions_cluster,
                    col.name = 'predictions_cluster')

saveRDS(data, file = "pilot/data_object_sct_integrated.rds")

# plot UMAPs
png("pilot/UMAP_labelTransfer_subclassAllan_sct_integrated.png")
DimPlot(data, reduction = "umap", group.by = "predictions_subclass", 
        cols = colorRampPalette(brewer.pal(9, "Set1"))(nlevels(as.factor(data$predictions_subclass))))
dev.off()

png("pilot/UMAP_labelTransfer_clusterAllan_sct_integrated.png", width = 2000, height = 1000)
DimPlot(data, reduction = "umap", group.by = "predictions_cluster",
        cols = colorRampPalette(brewer.pal(9, "Set1"))(nlevels(as.factor(data$predictions_cluster))))
dev.off()

png("pilot/UMAP_louvainCluster_sct_integrated.png")
DimPlot(data, reduction = "umap", group.by = "seurat_clusters",
        cols = colorRampPalette(brewer.pal(9, "Set1"))(nlevels(as.factor(data$seurat_clusters))))
dev.off()