Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/sctyner/geomnet

Examples and data for geom_net
https://github.com/sctyner/geomnet

cran ggplot2 networks plotly visualization

Last synced: about 1 month ago
JSON representation

Examples and data for geom_net

Awesome Lists containing this project

README 

        
---

output: github_document

---



# geomnet 



[![CRAN Status](http://www.r-pkg.org/badges/version/geomnet)](https://cran.r-project.org/package=geomnet)

[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/geomnet)](https://www.r-pkg.org/pkg/geomnet)

[![Travis-CI Build Status](https://travis-ci.org/sctyner/geomnet.svg?branch=master)](https://travis-ci.org/sctyner/geomnet)



`geomnet` is a package built on top of the most recent major `ggplot2` release. It provides a `ggplot2` `geom` called `geom_net` to visualize graphs and networks. It also include the function `stat_net` to calculate network layouts with the `sna` package. Finally, the function `geom_circle` is included to draw circles using `ggplot2`.



You can install `geomnet` directly from CRAN

`install.packages('geomnet')`

or from Github

`devtools::install_github("sctyner/geomnet")`



```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-"

)

```



# Examples



## `ggplot2` Theme Elements



This example shows the theme inheritance properties of the theme elements of `ggplot2`. Note: this example has not been updated since the release of `ggplot2 2.2.0` and as such the content may have changed. 



```{r theme, fig.align='center', message=FALSE, warning=FALSE}

library(dplyr)

library(geomnet)

data(theme_elements)

# data step

TEnet <- fortify(as.edgedf(theme_elements$edges[,c("parent", "child")]), theme_elements$vertices)

# create a degree variable for use later

TEnet <- TEnet %>%

  group_by(from_id) %>%

  mutate(degree = sqrt(10 * n() + 1))

# plot

ggplot(data = TEnet,

       aes(from_id = from_id, to_id = to_id)) +

  geom_net(layout.alg = "fruchtermanreingold",

    aes(fontsize = degree), directed = TRUE,

    labelon = TRUE, size = 1, labelcolour = 'black',

    ecolour = "grey70", arrowsize = 0.5,

    linewidth = 0.5, repel = TRUE) +

  theme_net() +

  xlim(c(-0.05, 1.05))

```



## Blood Donation Diagram



In this example, we reimagine the [traditional blood donation diagram](http://www.redcrossblood.org/learn-about-blood/blood-types) as a directed network. Arrows point to the blood type that receives. This example provides two data frames to `geom_net()`.  



```{r blood, fig.align='center'}

library(geomnet)

data(blood)

ggplot(data = blood$edges, aes(from_id = from, to_id = to)) +

  geom_net(colour = "darkred", layout.alg = "circle", labelon = TRUE, 

           size = 15, directed = TRUE, vjust = 0.5, labelcolour = "grey80",

           arrowsize = 1.5, linewidth = 0.5, arrowgap = 0.05,

           selfloops = TRUE, ecolour = "grey40") + 

  theme_net() 

```



## Harry Potter Peer Support Network



In this fun example from [this website](http://www.stats.ox.ac.uk/~snijders/siena/siena.html), there is a tie between two students if one provides emotional support to the other at some point in the book. It is a directed network, so in the visualization, the arrow points to the student receiving support. 



```{r HP, echo = FALSE, message=FALSE, warning=FALSE}

library(dplyr)

temp <- tempfile()

download.file("http://www.stats.ox.ac.uk/~snijders/siena/bossaert_meidert_harrypotter.zip",temp)

hp1 <- read.table(unz(temp, "hpbook1.txt"))

hp1 <- as.matrix(hp1)

diag(hp1) <- 0

hp1 <- data.frame(hp1)

hp1$id <- 1:64

hp1 <- hp1 %>% tidyr::gather(var, value, -id) %>%

               dplyr::filter(value == 1) %>% 

               dplyr::select(-value) %>% 

               dplyr::mutate(var = readr::parse_number(var), book = 1) %>% 

               dplyr::rename(from = id, to = var)

hp2 <- read.table(unz(temp, "hpbook2.txt"))

hp2 <- as.matrix(hp2)

diag(hp2) <- 0

hp2 <- data.frame(hp2)

hp2$id <- 1:64

hp2 <- hp2 %>% tidyr::gather(var, value, -id) %>%

               dplyr::filter(value == 1) %>% 

               dplyr::select(-value) %>% 

               dplyr::mutate(var = readr::parse_number(var), book = 2) %>% 

               dplyr::rename(from = id, to = var)

hp3 <- read.table(unz(temp, "hpbook3.txt"))

hp3 <- as.matrix(hp3)

diag(hp3) <- 0

hp3 <- data.frame(hp3)

hp3$id <- 1:64

hp3 <- hp3 %>% tidyr::gather(var, value, -id) %>%

               dplyr::filter(value == 1) %>% 

               dplyr::select(-value) %>% 

               dplyr::mutate(var = readr::parse_number(var), book = 3) %>% 

               dplyr::rename(from = id, to = var)

hp4 <- read.table(unz(temp, "hpbook4.txt"))

hp4 <- as.matrix(hp4)

diag(hp4) <- 0

hp4 <- data.frame(hp4)

hp4$id <- 1:64

hp4 <- hp4 %>% tidyr::gather(var, value, -id) %>%

               dplyr::filter(value == 1) %>% 

               dplyr::select(-value) %>% 

               dplyr::mutate(var = readr::parse_number(var), book = 4) %>% 

               dplyr::rename(from = id, to = var)

hp5 <- read.table(unz(temp, "hpbook5.txt"))

hp5 <- as.matrix(hp5)

diag(hp5) <- 0

hp5 <- data.frame(hp5)

hp5$id <- 1:64

hp5 <- hp5 %>% tidyr::gather(var, value, -id) %>%

               dplyr::filter(value == 1) %>% 

               dplyr::select(-value) %>% 

               dplyr::mutate(var = readr::parse_number(var), book = 5) %>% 

               dplyr::rename(from = id, to = var)

hp6 <- read.table(unz(temp, "hpbook6.txt"))

hp6 <- as.matrix(hp6)

diag(hp6) <- 0

hp6 <- data.frame(hp6)

hp6$id <- 1:64

hp6 <- hp6 %>% tidyr::gather(var, value, -id) %>%

               dplyr::filter(value == 1) %>% 

               dplyr::select(-value) %>% 

               dplyr::mutate(var = readr::parse_number(var), book = 6) %>% 

               dplyr::rename(from = id, to = var)

hp <- rbind(hp1, hp2, hp3, hp4, hp5, hp6)

hp.attributes <- read.table(unz(temp, "hpattributes.txt"), header=TRUE, stringsAsFactors = F)

hp.names <- read.table(unz(temp, "hpnames.txt"), header=TRUE, stringsAsFactors = F)

hp.names[,1] <- as.integer(hp.names[,1])

hp.1 <- merge(hp, hp.names, by.x = "from", by.y = "id")

names(hp.1)[4] <- "name1"

hp.2 <- merge(hp.1, hp.names, by.x = "to", by.y = "id")

names(hp.2)[5] <- "name2"

hp.edges <- hp.2[, c("name1", "name2", "book")] %>% dplyr::arrange(book, name1, name2)

hp.chars <- merge(hp.names, hp.attributes)

hp.chars$house <- factor(hp.chars$house, labels = c("Gryffindor", "Hufflepuff", "Ravenclaw", "Slytherin"))

hp.chars$gender <- factor(hp.chars$gender, labels = c("M", "F"))

unlink(temp)

hp.chars <- hp.chars[,-1]

```



```{r HPplot, fig.width=10, fig.height=8, fig.align='center', warning = FALSE}

library(geomnet)

head(hp.edges)

head(hp.chars)

hp.all <- fortify(as.edgedf(hp.edges), hp.chars, group = "book")

# only plot the characters with any connections in a given book. 

ggplot(data=hp.all, aes(from_id = from, to_id = to_id)) + 

  geom_net(fiteach=T, directed = T, size = 3, linewidth = .5, 

           ealpha = .5, labelon = T, fontsize = 3, repel = T, 

           labelcolour = "black", arrowsize = .5, singletons = FALSE,

           aes(colour = house, group = house, shape = gender)) + 

  scale_colour_manual(values = c("#941B08","#F1F31C", 

                                 "#071A80", "#154C07")) + 

  facet_wrap(~book, labeller = "label_both") + 

  theme_net() + theme(panel.background = element_rect(colour = 'black'))

```



## Interactivity with `plotly`!



Now including interactivity with `ggplotly()`!



```{r football, eval = FALSE}

# blood donation example

library(geomnet)

# devtools::install_github("ropensci/plotly")

library(plotly)

data(blood)

bloodnet <- fortify(as.edgedf(blood$edges), blood$vertices)

p <- ggplot(data = bloodnet, aes(from_id = from_id, to_id = to_id))



# create data plot

p2 <- p + geom_net(aes(size=Predominance, colour=type, shape=rho, linetype=group_to),

             linewidth=0.75, labelon =TRUE, directed = TRUE, labelcolour="black") +

  facet_wrap(~Ethnicity) +

  scale_colour_brewer(palette="Set2") 

ggplotly(p2) %>% hide_legend()



# Classic College Football Example

data("football")

# data step: merge vertices and edges

ftnet <- fortify(as.edgedf(football$edges), football$vertices)



# create data plot

gg <- ggplot(data = ftnet,

       aes(from_id = from_id, to_id = to_id)) +

  geom_net(layout.alg = 'fruchtermanreingold',

    aes(colour = value, group = value,

        linetype = factor(same.conf != 1)),

    linewidth = 0.5,

    size = 5, vjust = -0.75, alpha = 0.3) +

  theme_net() +

  theme(legend.position = "bottom") +

  scale_colour_brewer("Conference", palette = "Paired")  +

  guides(linetype = FALSE)

ggplotly(gg)

```