Network_plotting_with_R.Rmd

---
title: "Network plotting with Rstudio"
subtitle: "⚔<br/>presentation powered by xaringan"
author: "Gaspar Jekely"
institute: "RStudio course - LSI <br> 25-26th April 2022"
output:
  xaringan::moon_reader:
    css: addons/xaringan-themer-GJ.css
    nature:
      ratio: "16:9"
      beforeInit: ["addons/macros.js"]
      highlightStyle: github
      highlightLines: true
      countIncrementalSlides: true
      slideNumberFormat: "%current%"
      navigation:
        scroll: true
---


```{r xaringanExtra, echo=FALSE}
xaringanExtra::use_xaringan_extra(c("tile_view", "animate_css", "tachyons"))
#to load xaringanExtra in a single call
```

```{r xaringan-editable, echo=FALSE}
xaringanExtra::use_editable(expires = 1)
#makes slides editable  to make a component of your slides editable, use the .can-edit[] class.

```

```{r xaringan-scribble, echo=FALSE}
xaringanExtra::use_scribble()
#to draw on slides
```

```{r xaringan-panelset, echo=FALSE}
xaringanExtra::use_panelset()
#to add panels to slides with
#.panel[.panel-name[NAME]
#...content...
#]
```

---
# Network plotting - Create a matrix

``` {r, eval=TRUE}
library(tidyverse)
m <- matrix(c(1,2,3,0,0,3,11,4,0,1,0,3,4,5,6,7), nrow=4)
m
```
--
``` {r, eval=TRUE}
rownames(m) <- c('IN1','PRC','IN2','SN1')
m
```
--
``` {r, eval=TRUE}
colnames(m) <- c('IN1','PRC','IN2','SN1')
m
```

---
# Convert to tibble

``` {r, eval=TRUE}
tb <- as.data.frame(m) %>%
  rownames_to_column(var = "presyn_cell") %>%
  pivot_longer(-presyn_cell, names_to = "postsyn_cell", values_to = "synapses")
tb
```

---
# Plot with ggplot

``` {r, eval=TRUE, fig.height=6}
tb %>%
  ggplot(aes(x=presyn_cell, y=postsyn_cell, size = synapses, color = synapses)) +
  geom_point() +
  theme_minimal()

```
---
#Mutate

```{r, eval=TRUE}
tb <- tb %>%
  group_by(presyn_cell) %>%
  mutate(synapse_fraction = synapses / sum(synapses, na.rm = TRUE))
tb
```

---
# Plot with ggplot

``` {r, eval=TRUE, fig.height=6}
tb %>%
  ggplot(aes(x=presyn_cell, y=postsyn_cell, size = sqrt(synapses), color = synapse_fraction)) +
  geom_point() +
  theme_minimal()

```
 
---

```{r eval=TRUE}
library(igraph)
library(visNetwork)
library(tidygraph)
```
---
## convert to VisNetwork via tbl graph (works with all igraph methods)

```{r eval=TRUE}
g.visn <- tb %>%
  as_tbl_graph %>%
  toVisNetworkData()

g.visn 

## we can assign color to nodes
g.visn$nodes$color <- c("#E69F00", "#56B4E9", "#009E73", "#F0E442")
```

---

```{r eval=TRUE, fig.height=3}
visNet <- visNetwork(g.visn$nodes,g.visn$edges)%>% 
    visIgraphLayout(layout = "layout_nicely", physics = TRUE, randomSeed = 42) %>%
    visPhysics(solver = "forceAtlas2Based",
               forceAtlas2Based = list(gravitationalConstant = -400))%>%
    visEdges(smooth = list(type = 'curvedCW', roundness=0.1),
             scaling=list(min=2, max=8),
             color = list(inherit=TRUE, opacity=0.7),
             arrows = list(to = list(enabled = TRUE, 
                                     scaleFactor = 1.2, type = 'arrow'))) %>%
    visNodes(borderWidth=0.3, 
             color = list(background=g.visn$nodes$color, border='black'),
             opacity=0.9,
             shape='dot', 
             font=list(color='black', size=24),
             scaling = list(label=list(enabled=TRUE, min=16, max=28))) %>%
    visOptions(highlightNearest = TRUE) %>%
    visInteraction(dragNodes = TRUE, dragView = TRUE,
                   zoomView = TRUE, hover=TRUE,
                   multiselect=TRUE) %>%
    addFontAwesome()
   
visNet
```

---
# Read adjacency matrix

```{r eval=TRUE, fig.height=5}
adj <- read_csv("assets/data/adjacency_matrix.csv")

```

---
# Tidy it up

```{r eval=TRUE}
adj_tb <- adj %>%
  rename(presyn_cell=Neurons) %>%
  pivot_longer(-presyn_cell, names_to = "postsyn_cell", values_to = "synapses") 
adj_tb
```

---
# Plot

```{r eval=TRUE, fig.height=5}
adj_tb %>%
  ggplot(aes(x=presyn_cell, y=postsyn_cell, size = sqrt(synapses), color = synapses)) +
  geom_point() +
  theme_minimal()

```

---
# Convert to network with tidygraph package (gives an iGraph object), then tp VisNetwork

```{r eval=TRUE}
library(tidygraph)

g.visn <- adj_tb %>%
  as_tbl_graph %>%
  toVisNetworkData()
```

## define edge weights as 'values' 
```{r eval=TRUE}

g.visn$edges$value <- g.visn$edges$synapses
```
---
# visNetwork plot
```{r eval=TRUE}
visNet <- visNetwork(g.visn$nodes,g.visn$edges)%>% 
    visIgraphLayout(layout = "layout_nicely", physics = TRUE, randomSeed = 42) %>%
  visPhysics(solver = "forceAtlas2Based",
               forceAtlas2Based = list(gravitationalConstant = -400))%>%
    visEdges(smooth = list(type = 'curvedCW', roundness=0.1),
             scaling=list(min=2, max=8),
             color = list(inherit=TRUE, opacity=0.7),
             arrows = list(to = list(enabled = TRUE, 
                                     scaleFactor = 1.2, type = 'arrow'))) %>%
    visNodes(borderWidth=0.3, 
             color = list(background=g.visn$nodes$color, border='black'),
             opacity=0.9,
             shape='dot', 
             font=list(color='black', size=24),
             scaling = list(label=list(enabled=TRUE, min=16, max=28))) %>%
    addFontAwesome()

```

---
# show graph
```{r eval=TRUE}
visNet
```

---