metpath/vignettes/kegg_pathway_enrichment.Rmd at f48a36411ded0839c36f4cdd5d331476f1cbf977 · tidymass/metpath · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
---
title: "KEGG pathway enrichment"
author:
- name: Xiaotao Shen PhD (https://www.shenxt.info/)
date: "Created on 2020-03-28 and updated on `r Sys.Date()`"
output:
  html_document:
    df_print: paged
    toc: no
  pdf_document:
    toc: no
vignette: >
  %\VignetteIndexEntry{KEGG pathway enrichment}
  %\VignettePackage{metpath}
  %\VignetteEngine{knitr::rmarkdown}
  %\usepackage[utf8]{inputenc}
  %\VignetteEncoding{UTF-8}
---

```{r, include=FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%"
)
```

# **Load packages**

```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
library(metpath)
library(tidyverse)
```

# **Load KEGG pathway human database**

```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
data("kegg_hsa_pathway", package = "metpath")
kegg_hsa_pathway
```
```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
get_pathway_class(kegg_hsa_pathway)
```

# **Pathway enrichment**

We use the demo compound list from `metpath`.

```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
data("query_id_kegg", package = "metpath")
query_id_kegg
```

Remove the disease pathways:

```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
#get the class of pathways
pathway_class =
  metpath::pathway_class(kegg_hsa_pathway)

head(pathway_class)

remain_idx =
  pathway_class %>%
  unlist() %>%
  stringr::str_detect("Disease") %>%
  `!`() %>%
  which()

remain_idx

pathway_database =
  kegg_hsa_pathway[remain_idx]

pathway_database
```


```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
result =
enrich_kegg(query_id = query_id_kegg,
            query_type = "compound",
            id_type = "KEGG",
            pathway_database = pathway_database,
            p_cutoff = 0.05,
            p_adjust_method = "BH",
            threads = 3)
```

Check the result:

```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
result
```


# **Plot to show pathway enrichment**

```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
enrich_bar_plot(object = result)
```

```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
enrich_scatter_plot(object = result)
```

```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
enrich_network(object = result)
```


# **Session information**

```{r,eval = TRUE,warning=FALSE, message=FALSE,R.options="",cache=TRUE}
sessionInfo()
```