---
title: "Exploration"
author: "Audrey"
date: "`r format(Sys.time(), '%Y-%m-%d')`"
output:
  html_document:
    code_folding: show
    code_download: true
    toc: true
    toc_float: true
---

<style>
body {
text-align: justify}
</style>

The goal of this script is to explore *Ptcra* expression in our dataset. This gene has been described by [Toto et al. (once)](https://the_link).

# Environment

## Libraries

We load the libraries of interest :

```{r library, message = FALSE, warning = FALSE}
library(Seurat)
library(ggplot2)

.libPaths()
```

## Data

**Note** ! Data were previously prepared using the following code :

```{r prepare_data, eval = FALSE}
sobj = readRDS("/shared/projects/2325_ebaii/SingleCell/TD_DATA/DATA_START/CLUSTERING/TD3A.TDCT_Scal2K.IntH20.RDS")
sobj = Seurat::RunPCA(sobj)
sobj = Seurat::RunTSNE(sobj)
sobj = sobj[, 1:200]
saveRDS(sobj, file = "/shared/projects/2325_ebaii/SingleCell/TD_RMDs/Introduction_Rmd/sobj.RDS")
```

We load data :

```{r load_sobj}
sobj = readRDS("/shared/projects/2325_ebaii/SingleCell/TD_RMDs/Introduction_Rmd/sobj.RDS")
sobj
```


# Analysis

We visualize our favorite gene :

```{r see_ptcra, fig.width = 8, fig.height = 8}
Seurat::FeaturePlot(sobj, reduction = "tsne", features = "Ptcra") +
  ggplot2::theme(aspect.ratio = 1)
```

Which cells are positive for Ptcra ?

```{r binarize_ptcra}
sobj$is_Ptcra_pos = (Seurat::FetchData(sobj, "Ptcra")[, 1] > 0)
head(sobj$is_Ptcra_pos)
```

We visualize the positive and negative cells :

```{r see_bin_ptcra, fig.width = 8, fig.height = 8}
Seurat::DimPlot(sobj, reduction = "tsne", group.by = "is_Ptcra_pos") +
  ggplot2::theme(aspect.ratio = 1)
```

How many cells are positive ?

```{r count_bin_ptcra}
table(sobj$is_Ptcra_pos)
```

Half of cells are *Ptcra*+.

# Save

Eventually here, we can save the dataset that has been processed through this notebook.

```{r save_sobj, eval = FALSE}
saveRDS(sobj, file = "/shared/projects/2325_ebaii/SingleCell/TD_RMDs/Introduction_Rmd/sobj_processed.rds")
```


# R Session

```{r sessioninfo, echo = FALSE}
sessionInfo()
```