NPJ-GBM-PFB_code/stromal_integration.Rmd at main · plezar/NPJ-GBM-PFB_code · GitHub

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---
title: "Stromal_integration"
author: "Maksym"
date: "3/8/2023"
output: html_document
---

```{r}
library(Seurat)
library(SeuratData)
library(SeuratWrappers)
library(tidyverse)
```

Load data
```{r}
lgpt = readRDS("/Volumes/TOSHIBA/TIMElab/SCPCP000002/stromal_cells.rds")
meningioma = readRDS("/Volumes/TOSHIBA/TIMElab/Wang_Meningioma/stromal_cells.rds")
nf = readRDS("/Volumes/TOSHIBA/TIMElab/GSE163028_RAW/stromal_cells.rds")
mets = readRDS("/Volumes/TOSHIBA/TIMElab/GSE186344/stromal_cells.rds")
gbm = readRDS("/Volumes/TOSHIBA/TIMElab/GSE182109_processed/muralcells.rds")
DefaultAssay(gbm) <- "RNA"
```

```{r}
meningioma$cell.type <- meningioma$Final_celltype
mets$cell.type <- mets$Cell_Type
gbm$cell.type <- gbm$cell.type.fine
```

```{r}
overlapping_genes = Reduce(intersect, list(
  rownames(lgpt),
  rownames(meningioma),
  rownames(nf),
  rownames(mets),
  rownames(gbm)
))
```

```{r}
count_data = cbind(
  lgpt@assays$RNA@counts[overlapping_genes,],
  meningioma@assays$RNA@counts[overlapping_genes,],
  #nf@assays$RNA@counts[overlapping_genes,],
  mets@assays$RNA@counts[overlapping_genes,],
  gbm@assays$RNA@counts[overlapping_genes,]
  )
```

```{r}
metadata = rbind(
  lgpt@meta.data %>% select(cell.type) %>% mutate(Dataset = "PLGG"),
  meningioma@meta.data %>% select(cell.type) %>% mutate(Dataset = "Meningioma"),
  #nf@meta.data %>% select(cell.type),
  mets@meta.data %>% select(cell.type) %>% mutate(Dataset = "BMets"),
  gbm@meta.data %>% select(cell.type) %>% mutate(Dataset = "GBM")
)
```

```{r}
seurat_obj = CreateSeuratObject(
  counts = count_data,
  meta.data = metadata
)

nf = CreateSeuratObject(
  counts = nf@assays$RNA@counts[overlapping_genes,],
  meta.data = nf@meta.data %>% select(cell.type) %>% mutate(Dataset = "NF")
)
```

```{r}
seurat_obj <- NormalizeData(seurat_obj)
seurat_obj <- merge(seurat_obj, y = nf)
table(seurat_obj$Dataset)
```

```{r}
rm(lgpt, meningioma, nf, mets, gbm)
```

```{r}
seurat_obj <- FindVariableFeatures(seurat_obj)

seurat_obj_integrated <- RunFastMNN(object.list = SplitObject(seurat_obj, split.by = "Dataset"))
seurat_obj_integrated <- RunUMAP(seurat_obj_integrated, reduction = "mnn", dims = 1:15)
seurat_obj_integrated <- FindNeighbors(seurat_obj_integrated, reduction = "mnn", dims = 1:15)
seurat_obj_integrated <- FindClusters(seurat_obj_integrated)
```

```{r}
DimPlot(seurat_obj_integrated, group.by = c("Dataset"), label = T)
DimPlot(seurat_obj_integrated, group.by = c("cell.type"), label = T)
```

```{r}
saveRDS(seurat_obj_integrated, "/Volumes/TOSHIBA/TIMElab/stromal_integration.rds")
```