README.md

In RMHogervorst/gephi: Write graph objects to a file format that gephi understands

gephi

This is a simple package to export files into a csv format that gephi can understand. This package does not interface with the open source network vizualisation software gephi but it writes and reads in the same csv format as gephi.

I’ve found the need to convert tidygraph/igraph objects into a node and edge csv, to visualize in gephi quite often. This task should be trivial, but gephi is a bit particular and wants specific column names.

What does the package do?

Writes igraph files to csv format that gephi likes. Really? Gephi reads csv files just fine! Sure but it wants the columns in a particular order and named Source, Target etc. Let’s not do this by hand everytime: AUTOMATE THE BORING STUFF! HACK THE PLANET!

Installation

Install this developmental version with:

# install.packages("devtools")
devtools::install_github("RMHogervorst/gephi")

Example

• igraph to csv
• tidygraph to csv
• dataframe to csv

Writing out an igraph file to csv:

library(gephi) # includes the graphexample file
library(igraph)
#> 
#> Attaching package: 'igraph'
#> The following objects are masked from 'package:stats':
#> 
#>     decompose, spectrum
#> The following object is masked from 'package:base':
#> 
#>     union
V(graphexample)
#> + 5/5 vertices, named, from b833ca0:
#> [1] a d b c f
E(graphexample)
#> + 5/5 edges from b833ca0 (vertex names):
#> [1] a->b a->c a->d d->b d->f
gephi_write_edges(graphexample, "edges.csv")
#> writing edgesgraphexample
#> to edgefile: edges.csv/n

Technically an tidygraph object is also an igraph object so the writing will work the same.

library(gephi)
library(tidygraph)
#> 
#> Attaching package: 'tidygraph'
#> The following object is masked from 'package:igraph':
#> 
#>     groups
#> The following object is masked from 'package:stats':
#> 
#>     filter

(tidy_graphexample <- tidygraph::as_tbl_graph(graphexample)) # Just to show where this function comes from
#> # A tbl_graph: 5 nodes and 5 edges
#> #
#> # A directed acyclic simple graph with 1 component
#> #
#> # Node Data: 5 x 2 (active)
#>   name  color 
#>   <chr> <chr> 
#> 1 a     blue  
#> 2 d     red   
#> 3 b     blue  
#> 4 c     blue  
#> 5 f     yellow
#> #
#> # Edge Data: 5 x 3
#>    from    to weight
#>   <int> <int>  <dbl>
#> 1     1     3      1
#> 2     1     4      1
#> 3     1     2      1
#> # … with 2 more rows

More specifically if you want to modify your graph and visualize a subset in gephi, here is a tidygraph worked example where I select only the edges that are blue, add a new edge property and write the resulting graph to csv:

tidy_graphexample %>%  # but the igraph object works just as well
    activate(nodes) %>% 
    filter(color == "blue") %>% 
    activate(edges) %>% 
    mutate(dongle = "dingle") %>% 
    gephi_write_edges("edges_subset.csv") %>% 
    print()
#> writing edges.
#> to edgefile: edges_subset.csv/n
#> # A tbl_graph: 3 nodes and 2 edges
#> #
#> # A rooted tree
#> #
#> # Edge Data: 2 x 4 (active)
#>    from    to weight dongle
#>   <int> <int>  <dbl> <chr> 
#> 1     1     2      1 dingle
#> 2     1     3      1 dingle
#> #
#> # Node Data: 3 x 2
#>   name  color
#>   <chr> <chr>
#> 1 a     blue 
#> 2 b     blue 
#> 3 c     blue

But is is also possible to write a set of edges when there is no graph object, just a dataframe.

a_nice_df <- data.frame(
    start = c(1,2,3,4,5,6,7),
    finish = c(2,4,4,7,2,1,3),
    weight = c(1,1,1,2,6,1,1)
)
print(a_nice_df) 
#>   start finish weight
#> 1     1      2      1
#> 2     2      4      1
#> 3     3      4      1
#> 4     4      7      2
#> 5     5      2      6
#> 6     6      1      1
#> 7     7      3      1
gephi_write_edges_from_df(a_nice_df, path = "edges2.csv")
#> writing edges from dataframe to edgefile: edges2.csv

Test coverage statistics

covr::package_coverage(type = "tests")
#> 
#> files differ in number of lines:
#> gephi Coverage: 32.00%
#> R/writing_tools.R: 18.75%
#> R/utils.R: 42.86%
#> R/read_tools.R: 100.00%

cleaning up after ourselves for this demo

file.remove("edges.csv")
#> [1] TRUE
file.remove("edges2.csv")
#> [1] TRUE
file.remove("edges_subset.csv")
#> [1] TRUE

Links

• Gephi (the graph visualisation software, not this interface) website

RMHogervorst/gephi documentation built on July 9, 2022, 6:50 a.m.