## ----message=F, warning=F, results=F------------------------------------------
library(scRNAseq)

lung <- ZilionisLungData()
immune <- lung$Used & lung$used_in_NSCLC_immune
lung <- lung[,immune]
lung <- lung[,1:5000]

exp.mat <- Matrix::Matrix(counts(lung),sparse = TRUE)

## -----------------------------------------------------------------------------
signatures <- list(
    Tcell = c("CD3D","CD3E","CD3G","CD2","TRAC"),
    Myeloid = c("CD14","LYZ","CSF1R","FCER1G","SPI1","LCK-"),
    NK = c("KLRD1","NCAM1","NKG7","CD3D-","CD3E-"),
    Plasma_cell = c("IGKC","IGHG3","IGHG1","IGHA1","CD19-")
)

## ----message=F, warning=F-----------------------------------------------------
library(UCell)
library(Seurat)
seurat.object <- CreateSeuratObject(counts = exp.mat, 
                                    project = "Zilionis_immune")
seurat.object <- AddModuleScore_UCell(seurat.object, 
                                      features=signatures, name=NULL)
head(seurat.object[[]])

## ----message=F, warning=F-----------------------------------------------------
seurat.object <- NormalizeData(seurat.object)
seurat.object <- FindVariableFeatures(seurat.object, 
                     selection.method = "vst", nfeatures = 500)
  
seurat.object <- ScaleData(seurat.object)
seurat.object <- RunPCA(seurat.object, npcs = 20, 
                        features=VariableFeatures(seurat.object)) 
seurat.object <- RunUMAP(seurat.object, reduction = "pca", 
                         dims = 1:20, seed.use=123)

## ----fig.width=9, fig.height=7, dpi=60----------------------------------------
library(ggplot2)
library(patchwork)

FeaturePlot(seurat.object, reduction = "umap", features = names(signatures))

## -----------------------------------------------------------------------------
seurat.object <- SmoothKNN(seurat.object,
                           signature.names = names(signatures),
                           reduction="pca")

## ----fig.wide=TRUE, dpi=60----------------------------------------------------
FeaturePlot(seurat.object, reduction = "umap", features = c("NK","NK_kNN"))

## -----------------------------------------------------------------------------
genes <- c("CD2","CSF1R")

expr <- Seurat::GetAssayData(seurat.object, assay="RNA", slot="data")[genes,]
expr <- t(as.matrix(expr))
seurat.object <- AddMetaData(seurat.object, metadata=as.data.frame(expr))

## ----warning=FALSE, fig.width=9, fig.height=7, dpi=60-------------------------
seurat.object <- SmoothKNN(seurat.object, signature.names=genes,
                           reduction="pca", k=20, suffix = "_smooth")

FeaturePlot(seurat.object, reduction = "umap",
            features = c("CD2","CD2_smooth","CSF1R","CSF1R_smooth"))

## -----------------------------------------------------------------------------
sessionInfo()