analysis_1.Rmd

---
title: "analysis_1"
author: "Irzam Sarfraz"
date: "`r Sys.Date()`"
output: html_document
---

```{r}
# Based on accessibility, are mutations enriched in peaks of some cell-type 


library(singleCellTK)
```

```{r}
# scATAC-seq Hematopoeisis + MPAL cell x peak Summarized Experiment
data <- readRDS("/projectnb/paxlab/isarfraz/Greenleaf_Data_RDS/scATAC-All-Hematopoiesis-MPAL-191120.rds")
data <- as(data, "SingleCellExperiment")
```

```{r}
# UMAP1 and ProjectUMAP1 are different
# Here I am testing with ProjectUMAP1
umap1 <- colData(data)[["ProjectUMAP1"]]
umap2 <- colData(data)[["ProjectUMAP2"]]
umapProject <- data.frame(umap1 = umap1, umap2 = umap2)
reducedDim(data, "umapProject") <- umapProject
```

```{r}
# UMAP for umapProject
singleCellTK::plotSCEDimReduceColData(inSCE = data, colorBy = "ProjectClassification", reducedDimName = "umapProject", dim1 = "umap1", dim2 = "umap2")
```
```{r}
# UMAP1 and ProjectUMAP1 are different
# Here I am testing with UMAP1
umap1 <- colData(data)[["UMAP1"]]
umap2 <- colData(data)[["UMAP2"]]
umap <- data.frame(umap1 = umap1, umap2 = umap2)
reducedDim(data, "umap") <- umap
```

```{r}
# UMAP for umap
singleCellTK::plotSCEDimReduceColData(inSCE = data, colorBy = "ProjectClassification", reducedDimName = "umap", dim1 = "umap1", dim2 = "umap2")
```

```{r}
data
```

Need cell types

lets do seurat tutorial

```{r}
library(Seurat)

```