analysis.Rmd

---
title: "R Notebook"
output: html_notebook
---

```{r}
library(hash)
```


Read data
```{r}
data <- readRDS("./GSE149221_SpInteg.rds")
```

Get sample names
```{r}
samples <- c()
sample_list <- strsplit(Cells(data), "_")
for (i in 1:60399)
  samples <- append(samples, sample_list[[i]][1])
samples <- unique(samples)
samples
```
Get cells by sample 
```{r}
cells.Sp1 <- Cells(data)[grepl("Sp1_", Cells(data))]
cells.Sp2 <- Cells(data)[grepl("Sp2_", Cells(data))]
cells.Sp3 <- Cells(data)[grepl("Sp3_", Cells(data))]
cells.EB <- Cells(data)[grepl("EB_", Cells(data))]
cells.HB <- Cells(data)[grepl("HB_", Cells(data))]
cells.MB <- Cells(data)[grepl("MB_", Cells(data))]
cells.EG <- Cells(data)[grepl("EG_", Cells(data))]
cells.LG <- Cells(data)[grepl("LG_", Cells(data))]
```

```{r}
DimPlot(data, reduction = "tsne", cells=cells.Sp1, label=TRUE)
```

```{r}
VlnPlot(data, features = c("SoxB2"))
```

```{r}
DimPlot(data, reduction = "tsne", label=TRUE)
plot1 <- FeaturePlot(data, features = c("foxq2"), label=TRUE)
plot2 <- FeaturePlot(data, features = c("NK2.1"), label=TRUE)
plot3 <- FeaturePlot(data, features = c("AnkAT-1"), label=TRUE)
plot4 <- FeaturePlot(data, features = c("SoxB2"), label=TRUE)
plot5 <- FeaturePlot(data, features = c("Alx1"), label=TRUE)
plot5
grep("fox", rownames(data), value=TRUE)
```
```{r}

```