AUCell_intro.Rmd

---
title: "R Notebook"
output: html_notebook
---


```{r}
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AUCell")
```

```{r}
library(AUCell)
library(Seurat)
```

```{r}
load("droplet_Lung_seurat_tiss.Robj")
tiss <- UpdateSeuratObject(object = tiss)
```

```{r}
tiss[[]]
```

```{r}
DimPlot(object = tiss, group.by = "cell_ontology_class", label = TRUE)
```

```{r}
markers <- read.csv("PanglaoDB_markers_27_Mar_2020.tsv", sep = "\t")
markers <- markers[markers$cell.type == "Endothelial cells" & markers$species != "Hs",]
markers
```
```{r}
genes <- markers$official.gene.symbol

mousify <- function(a){
  return(paste0(substr(a,1,1), tolower(substr(a,2,nchar(a)))))
  
}
genes <- sapply(genes, mousify)
genes
```

```{r}
counts <- GetAssayData(object = tiss, slot = "counts")
```

```{r}
cell_rankings <- AUCell_buildRankings(counts)
```

```{r}
cells_AUC <- AUCell_calcAUC(genes, cell_rankings)
```


```{r}
cells_assignment <- AUCell_exploreThresholds(cells_AUC, plotHist = TRUE, assign=TRUE)
```

```{r}
cells_assignment$geneSet$assignment
```


```{r}
new_cells <- names(which(getAUC(cells_AUC)["geneSet",]>0.15))
```

```{r}
tiss$is_ec <- ifelse(colnames(tiss) %in% new_cells, "EC", "non_EC")
```

```{r}
tiss[[]]
```

```{r}
DimPlot(object = tiss, group.by = "is_ec", label = TRUE)
```

```{r}
DimPlot(object = tiss, group.by = "cell_ontology_class", label = TRUE)
```