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README.qmd
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---
format: markdown_github
---
```{r include=FALSE}
knitr::opts_chunk$set(fig.path = "man/figures/", warning = FALSE)
```
[](https://cran.r-project.org/package=rgexf)
[](https://cran.r-project.org/package=rgexf)
[](https://cran.r-project.org/package=rgexf)
[](https://github.com/gvegayon/rgexf/actions/workflows/ci.yml)
[](https://github.com/gvegayon/rgexf/actions/workflows/website.yml)
[](https://ci.appveyor.com/project/gvegayon/rgexf)
[](https://app.codecov.io/github/gvegayon/rgexf?branch=master)
[](https://doi.org/10.21105/joss.03456)
[](https://github.com/sponsors/gvegayon)
# rgexf: Build, Import and Export GEXF Graph Files <img src="man/figures/logo.svg" align="right" height="200"/>
The first R package to work with GEXF graph files (used in Gephi and
others). `rgexf` allows reading and writing graph files, including:
a. Nodes/edges attributes,
b. GEXF viz attributes (such as color, size, and position),
c. Network dynamics (for both edges and nodes, including spells) and
d. Edges weighting.
Users can build/handle graphs element-by-element or through data-frames,
visualize the graph on a web browser through ~~sigmajs javascript~~
[gexf-js](https://github.com/raphv/gexf-js) library and interact with
the igraph package.
```{r news, echo = FALSE, results='asis', }
x <- readLines("NEWS.md")
ids <- which(grepl("^#\\s*[a-zA-Z]",x))
ids <- ids[1:2] - c(0, 1)
cat(x[ids[1]:ids[2]], sep = "\n")
```
More in the [NEWS.md](NEWS.md) file.
# Installation
To install the latest version of `rgexf`, you can use `devtools`
```r
library(devtools)
install_github("gvegayon/rgexf")
```
The more stable (but old) version of `rgexf` can be found on CRAN too:
```
install.packages("rgexf")
```
# Citation
```{r, comment=""}
citation(package="rgexf")
```
# Examples
## Example 1: Importing GEXF files
We can use the `read.gexf` function to read GEXF files into R:
```{r read-lesmiserables}
# Loading the package
library(rgexf)
g <- system.file("gexf-graphs/lesmiserables.gexf", package="rgexf")
g <- read.gexf(g)
head(g) # Taking a look at the first handful
```
Moreover, we can use the `gexf.to.igraph()` function to convert the
`gexf` object into an `igraph` object:
```{r igraph}
library(igraph)
ig <- gexf.to.igraph(g)
op <- par(mai = rep(0, 4)) # Making room
plot(ig)
par(op)
```
Using the `plot.gexf` method--which uses the `gexf-js` JavaScript library--results in a Web visualization of the graph, like this:
```r
plot(g)
```
A live version of the figure is available [here](https://gvegayon.github.io/rgexf/lesmiserables/).
## Example 2: Static net ##
```{r}
# Creating a group of individuals and their relations
people <- data.frame(matrix(c(1:4, 'juan', 'pedro', 'matthew', 'carlos'),ncol=2))
people
```
```{r}
# Defining the relations structure
relations <- data.frame(matrix(c(1,4,1,2,1,3,2,3,3,4,4,2), ncol=2, byrow=T))
relations
```
```{r}
# Getting things done
write.gexf(people, relations)
```
## Example 3: Dynamic net ##
```{r}
# Defining the dynamic structure, note that there are some nodes that have NA at the end.
time<-matrix(c(10.0,13.0,2.0,2.0,12.0,rep(NA,3)), nrow=4, ncol=2)
time
```
```{r}
# Getting things done
write.gexf(people, relations, nodeDynamic=time)
```
## Example 4: More complex... Dynamic graph with attributes both for nodes and edges##
First, we define dynamics
```{r}
time.nodes<-matrix(c(10.0,13.0,2.0,2.0,12.0,rep(NA,3)), nrow=4, ncol=2)
time.nodes
time.edges<-matrix(c(10.0,13.0,2.0,2.0,12.0,1,5,rep(NA,5)), nrow=6, ncol=2)
time.edges
```
Now we define the attribute values
```{r}
# Defining a data frame of attributes for nodes and edges
node.att <- data.frame(letrafavorita=letters[1:4], numbers=1:4, stringsAsFactors=F)
node.att
edge.att <- data.frame(letrafavorita=letters[1:6], numbers=1:6, stringsAsFactors=F)
edge.att
# Getting the things done
write.gexf(nodes=people, edges=relations, edgeDynamic=time.edges,
edgesAtt=edge.att, nodeDynamic=time.nodes, nodesAtt=node.att)
```
# Code of Conduct
We welcome contributions to `rgexf`. Whether reporting a bug, starting a
discussion by asking a question, or proposing/requesting a new feature,
please go by creating a new issue
[here](https://github.com/gvegayon/rgexf/issues) so that we can talk
about it.
Please note that the rgexf project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms
# Session info
```{r}
devtools::session_info()
```