02-Enrichment.Rmd

```{r}
my_packages <- c("tidyverse", "data.table",
                 # "stringdist",
                 "clusterProfiler", "org.Hs.eg.db")
pacman::p_load(char = my_packages)

tmp <- list()
```


# Cluster Profile
```{r}
target_df4 <- readRDS(file = "Output/01/target_df4.Rds")
```


```{r}
marker <- bitr(target_df4$GeneNames, OrgDb = "org.Hs.eg.db", 
                   fromType = "SYMBOL", toType = "ENTREZID")
```

```{r}
GO <- enrichGO(gene = marker$ENTREZID,
                   OrgDb= org.Hs.eg.db,
                   ont = "ALL",
                   pAdjustMethod = "BH",
                   minGSSize = 1,
                   pvalueCutoff = 0.05,
                   readable = TRUE)
GO_df <- GO@result

KEGG <- enrichKEGG(gene = marker$ENTREZID,
                      organism     = 'hsa',
                      pvalueCutoff = 0.05,
                      qvalueCutoff =0.05)
KEGG_df <- KEGG@result
```

# Plot
GO:
```{r}
p4 <- barplot(GO, split = "ONTOLOGY") +
    facet_grid(ONTOLOGY~., scale = "free")
p4
```

```{r}
ggsave(plot = p4,
  filename = "Plot/p4.png",
  width = 10,             
  height = 12,           
  units = "in",         
  dpi = 600)
```


KEGG:
```{r}
p5 <- dotplot(KEGG, showCategory = 15)
p5
```

```{r}
ggsave(plot = p5,
  filename = "Plot/p5.png",
  width = 8,             
  height = 6,           
  units = "in",         
  dpi = 600)
```

```{r}
# vec_toll <- strsplit("841/6416/3553/3569/3576/5594/1432/5595/5599/4792/6696/207/6772/5970/7124", "/")[[1]]
# 
# toll_df <- marker[marker$ENTREZID %in% vec_toll,]
# toll_df
```