Example_Code.Rmd

---
title: "BM HCA MPAL transfer label"
output: html_notebook
---

This is an [R Markdown](http://rmarkdown.rstudio.com) Notebook. When you execute code within the notebook, the results appear beneath the code. 

Try executing this chunk by clicking the *Run* button within the chunk or by placing your cursor inside it and pressing *Cmd+Shift+Enter*. 

```{r}
rm(list=ls())

#Load neccessary packages
suppressPackageStartupMessages({
  library(monocle3)
  library(reticulate)
  library(dplyr)
  library(Matrix)
  library(ggplot2)
  library(xfun)
  library(pals)
  library(RColorBrewer)
  library(Seurat)
  library(ggplot2)
  library(parallel)
  library(scCustomize)
  library(SeuratObject)
  library(SeuratDisk)
  library(tibble)
  library(pbmcapply)
  library(viridis)
})

Sys.setenv('R_MAX_VSIZE'=32000000000)
#Sys.getenv()
```

#load HCA bone marrow data set
```{r}
hca.immune <- Connect(filename = "/Volumes/fh/scratch/delete90/furlan_s/owalt/BM_HCA/1M-immune-human-immune-10XV2.loom", mode = "r")
hca.seurat <- as.Seurat(hca.immune)
Idents(l6.seurat) <- "ClusterName"
VlnPlot(l6.seurat, features = c("Sparc", "Ftl1", "Junb", "Ccl4"), ncol = 2)
```

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