scRNA_pipeline_v1.Rmd

---
title: "scRNA_pipeline_v1"
author: Stephanie The
date: 6/13/19
output: html_document

---

Load required packages
``` {r setup, include = FALSE} 
library(Seurat)
library(dplyr)
library(magrittr)
library(pheatmap)
library(RColorBrewer)
library(scales)
library(data.table)

# Load umap
Sys.setenv(PATH= paste("C:/Users/Stephanie/Anaconda3/envs/r-reticulate/Library/bin",Sys.getenv()["PATH"],sep=";"))
Sys.setenv(RETICULATE_PYTHON = "C:/Users/Stephanie/Anaconda3/envs/r-reticulate/python.exe")
library(reticulate)
use_condaenv("r-reticulate")
py_config()
import("umap")
```

Load cell cycle genes (mouse or human choices only)
``` {r}
species <- readline(prompt = "What species are you working with?\n")

if (species == 'human') {
  s_genes <- cc.genes$s.genes
  g2m_genes <- cc.genes$g2m.genes
}
else {  # mouse
  readRDS(("~/Rao's Lab/Single Cell/single_cell/mouse_cell_cycle_genes/mouse_cell_cycle_genes.rds")
  s_genes <- mouse_cell_cycle_genes$s.genes
  g2m_genes <- mouse_cell_cycle_genes$g2m.genes
}
```

Load data and create Seurat objects (first time)
```{r}

n_files <- readline("How many files do you have? ")

files <- c()
files <- sapply(1:n_files, function(i) files <- c(files, choose.dir(caption = paste("Directory", i, 
                                                                                    sep = " "))))

# Save directories in case you want to go back to this step
fwrite(as.list(files), file = "directories.txt")




# Create Seurat objects
# names must in order of directories/data
object_names <- unlist(strsplit(readline(prompt = "Object names (separate by ', ')"),split = ', '))
project_names <- unlist(strsplit(readline(prompt = "Project names (separate by ', ')"),split = ', '))

object_list <- list()
object_list <- sapply(1:n_files, function(i) object_list <- append(object_list, object_names[i] = CreateSeuratObject(Read10X(files[i]), project = project_names[i], min.cells = 3, min.features = 100)))
```

Load data and create Seurat objects (after first time)
``` {r}
files <- c(fread(file.choose(), sep = ',', header = F, stringsAsFactors = F))
files <- unname(unlist(files))
```




```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

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