Pipeline_graph.Rmd

---
title: "Pipeline"
author: "Chenxin Li"
date: "2023-04-01"
output: html_notebook
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Package
```{r}
library(tidyverse)
library(readxl)
library(igraph)
library(ggraph)
library(RColorBrewer)
library(viridis)
library(rcartocolor)
```

# Data
```{r}
edge_table <- read_excel("../Data/Multi-ome_edges.xlsx")
node_table <- read_excel("../Data/Multi-ome_nodes.xlsx")

head(edge_table)
head(node_table)
```
## Reorder levels in node table
```{r}
node_table <- node_table %>% 
  mutate(Type = factor(Type, levels = c(
    "Input", "Upstream", "Intermediate", "R.Data", "Downstream"
  ))) %>% 
  mutate(txt.col = case_when(
    Type == "Input" |
      Type == "Upstream" |
      Type == "Intermediate"  ~ "White",
    T ~ "Black"
  ))
```


## Check if nodes match edge terminals 
```{r}
setdiff(
  unique(c(edge_table$From, edge_table$To)),
  node_table$Name
)
```


# Make network object 
```{r}
my_pipeline <- graph_from_data_frame(d = edge_table, 
                                     vertices = node_table, 
                                     directed = T)
```


# Graph pipeline as network
```{r}
my_pipeline %>% 
  ggraph(
    layout = "tree"
    ) +
  geom_edge_link(
    arrow = arrow(length = unit(0.4, 'lines')), 
    start_cap = circle(1.5, 'lines'),
    end_cap = circle(1.5, 'lines'),
    width = 1.2, alpha = 0.6, color = "grey30"
  ) +
  geom_node_point(aes(fill = Type, color = txt.col),
                 size = 3, shape = 21, alpha = 0.8) +
  geom_node_text(aes(label = name), alpha = 0.8, repel = T,
                 size = 4) +
  scale_fill_manual(values = viridis(5),
                     limits = c(
                        "Input", "Upstream", "Intermediate", "R.Data", "Downstream"
                     )) +
  scale_color_identity() +
  labs(fill = NULL) +
  theme_void() +
  theme(
    legend.position = c(0.8, 0.2)
  ) 

ggsave("../Results/Pipeline.svg", height = 6, width = 5, bg = "white")
ggsave("../Results/Pipeline.png", height = 6, width = 5, bg = "white")
```