data_dir = "/shared/projects/2422_ebaii_n1/atelier_scrnaseq/Intro_Rmd/"

# Load data
sobj = readRDS(paste0(data_dir, "sobj.rds"))
sobj

# Libraries of interest
library(Seurat)

# Visualize our favorite gene
FeaturePlot(sobj, reduction = "tsne", features = "Ptcra") +
  theme(aspect.ratio = 1)

# Ptcra is more expressed on the right, but how many cells are concerned ?

# Which cells are positive for Ptcra ?
library(ggplot2)

sobj$is_Ptcra_pos = (FetchData(sobj, "Ptcra")[, 1] > 0)
DimPlot(sobj, reduction = "tsne", group.by = "is_Ptcra_pos") +
  theme(aspect.ratio = 1)

# How many cells are positive ?
table(sobj$is_Ptcra_pos)

# half of cells are Ptcra+