Type:	Package
Title:	Manipulate and Visualize Graphs in the 'ribios' Software Suite
Version:	1.1.0
Date:	2026-01-24
Description:	Tools to manipulate and visualize graphs (networks) for computational biology in drug discovery, for instance functions for creating bipartite graphs and for interactive visualizations. Zhang (2025) https://github.com/bedapub/ribiosGraph.
Depends:	R (≥ 3.4.0), igraph
Imports:	magrittr, plotly, ribiosUtils
Suggests:	testthat
License:	GPL-3
URL:	https://github.com/bedapub/ribiosGraph
BugReports:	https://github.com/bedapub/ribiosGraph/issues
Encoding:	UTF-8
RoxygenNote:	7.3.3
NeedsCompilation:	no
Packaged:	2026-02-18 09:20:43 UTC; david
Author:	Jitao David Zhang [aut, cre]
Maintainer:	Jitao David Zhang <jitao_david.zhang@roche.com>
Repository:	CRAN
Date/Publication:	2026-02-20 10:40:14 UTC

Create a bipartite graph from data frame

Description

Create a bipartite graph from data frame

Usage

bipartite_graph_from_data_frame(x)

Arguments

Value

A igraph object that represents a bipartite graph. The type attribute of vertices is a logical vector that represents the two classes of nodes: nodes in the first column in the input data.frame are of the type TRUE, and those in the second column are of the type FALSE.

Extra columns besides the first two are used as edge attribtues. See example below.

Examples

myDataFrame <- data.frame(Alpha=c("A", "E", "O", "U", "B", "D"), 
  Type=c("Vowel", "Vowel", "Vowel", "Vowel", "Consonance", "Consonance"))
myBpGraph <- bipartite_graph_from_data_frame(myDataFrame)

myDataFrame2 <- data.frame(Alpha=c("A", "E", "O", "U", "B", "D"), 
  Type=c("Vowel", "Vowel", "Vowel", "Vowel", "Consonance", "Consonance"),
  Example=c("BAT", "BED", "BOT", "BUT", "DUB", "DUB"))
myBpGraph2 <- bipartite_graph_from_data_frame(myDataFrame2)
igraph::E(myBpGraph2)$Example

Export igraph object to GML, friendly to Cytoscape and yEd

Description

exportGML exports an igraph object to GML files complying with specifications defined by Cytoscape and yEd. Compared to the native write.graph function provided by the igraph package, GML files exported with exportGML can be directly read and properly visualized by Cytoscape and yEd.

Currently the function uses supports following attributes: Node name: V(igraph)$name Node label: V(igraph)$label Node isInput: V(igraph)$isInput, controlling node shapes Edge label: V(igraph)$label, determining edge target arrow

So far the function is mainly used by the ronet.Rscript script in the package. Users are invited to adapt the function for other purposes.

Usage

exportGML(igraph, filename)

Arguments

Value

Invisible NULL

Author(s)

Jitao David Zhang, jitao_david.zhang@roche.com

See Also

write.graph

Examples

 g <- barabasi.game(100, directed=FALSE)
 V(g)$label <- c(paste("node", 1:99, sep=""),"--")
 V(g)$name <- 1:100 
 V(g)$isInput <- rbinom(100,1, 0.5)
 E(g)$label <- "Expression"
 gPosE <- as.logical(rbinom(ecount(g), 1, 0.25))
 gNegE <- as.logical(rbinom(ecount(g), 1, 0.25))
 E(g)$label[gPosE] <- "Expressoion_Positive"
 E(g)$label[gNegE] <- "Expressoion_Negative"
 gFile <- tempfile()
 exportGML(g, gFile)

Build a bipartite graph with an incidence matrix

Description

Build a bipartite graph with an incidence matrix

Usage

incidence2bipartite(
  matrix,
  size = c(12, 9),
  color = c("orange", "lightblue"),
  label.cex = c(1.1, 0.95),
  label.color = c("black", "navyblue"),
  V = list(),
  E = list(color = "black")
)

Arguments

Value

An instance of igraph graph

Examples

myIncMat <- matrix(c(0, 0, 1, 
  0, 1, 0,
  1, 0, 0,
  0, 1, 1,
  1, 1, 1),
  ncol=3, byrow=TRUE, dimnames=list(LETTERS[1:5], letters[1:3]))
myGraph <- incidence2bipartite(myIncMat,
  size=c(18,12),
  V=list(shape=c("rectangle", "circle"),
         frame.color="lightgray"))
if(requireNamespace("igraph")) {
  igraph::plot.igraph(myGraph)
}

Layout a bipartite graph from left to right

Description

Layout a bipartite graph from left to right

Usage

layout_as_bipartiteLR(g)

Arguments

Value

A two-column matrix, the layout of the graph

The function simply calls layout_as_bipartite and reverses the X and Y coordinates.

Examples

myDataFrame <- data.frame(Alpha=c("A", "E", "O", "U", "B", "D"), 
  Type=c("Vowel", "Vowel", "Vowel", "Vowel", "Consonance", "Consonance"))
myBpGraph <- bipartite_graph_from_data_frame(myDataFrame)
myLayout <- layout_as_bipartiteLR(myBpGraph)

Convert a list of character strings into an incidence matrix

Description

Convert a list of character strings into an incidence matrix

Usage

list2incidenceMatrix(list, type = c("binary", "count"))

Arguments

Value

An incidence matrix, containing either binary (TRUE/FALSE) or integer values.

Type 'binary' will produce a logical matrix, whereas 'count' will produce a matrix where the frequency of the character strings in the list.

Author(s)

Jitao David Zhang, jitao_david.zhang@roche.com

Examples

wordList <- list("2006"=c("HSV", "BVB", "FCB"), 
  "2007"=c("BVB", "VFB", "STP"), 
  "2008"=c("VFL", "BVB", "HSV"))
list2incidenceMatrix(wordList, type="binary")

letterList <- list("First"=c("A", "a", "A", "a"), "Second"=c("B", "b", "A"))
list2incidenceMatrix(letterList, type="count")
list2incidenceMatrix(letterList, type="binary")

Plot a bipartite graph using plot_ly

Description

Plot a bipartite graph using plot_ly

Usage

plotlyBipartiteGraph(
  g,
  layout = layout_as_bipartiteLR(g),
  edge.line = list(color = "#030303", width = 0.3),
  axis = list(title = "", showgrid = FALSE, showticklabels = FALSE, zeroline = FALSE),
  title = ""
)

Arguments

Value

A plotly and htmlwidget object

If the layout is left-right, the function takes care of the alignment of labels

Examples

myDataFrame <- data.frame(word=c("ja", "nein", "yes", "no", "stark", "stark"),
  language=c("German", "German", "English", "English", "English", "German"))
myBpGraph <- bipartite_graph_from_data_frame(myDataFrame)
plotlyBipartiteGraph(myBpGraph)