Understanding RCyjs and Specifying Node Labels from Adjacency Matrix Columns

In this article, we will delve into the world of RCyjs, a powerful package for creating interactive graphs in R. We will explore how to specify node labels from adjacency matrix columns, a crucial aspect of graph visualization.

Introduction to RCyjs

RCyjs is a part of the graph package in R and provides an interface to Cytoscape, a widely used tool for visualizing complex networks. Cytoscape allows users to create interactive graphs that can be exported in various formats, including SVG, PNG, and PDF.

Creating an Adjacency Matrix

To work with RCyjs, we first need to create an adjacency matrix from our data. The adjacency matrix is a square matrix where the entry at row i and column j represents the weight of the edge between node i and node j. In our example, we use the cor function to calculate correlations between rows in the data.

# Load necessary libraries
library(graph)
library(RCyjs)
library(igraph)

# Read data from file
data <- read.table("text_file_containing_data.txt", sep="\t")

# Create an adjacency matrix
p1 <- cor(data[1:20,1:20], use="p")

Creating a GraphNEL

Next, we create a graphNEL, which is the base class for RCyjs graphs. We pass our adjacency matrix to the igraph.to.graphnel function to convert it into a graphNEL.

# Convert adjacency matrix to graphNEL
g <- igraph.to.graphnel(simplify(graph_from_adjacency_matrix(p1, weighted=T)), directed = TRUE)

Specifying Node Labels

Now that we have our graphNEL, we can specify node labels. The nodeDataDefaults function allows us to set default values for node attributes. In this case, we want to initialize the label attribute with an empty string.

# Initialize default node labels
nodeDataDefaults(g, attr="label") <- ""

However, in our example code, we used setNodeLabelRule, which is not correct. This function sets a rule for labeling nodes based on certain conditions. Instead, we need to use the nodeData function to assign specific labels to each node.

# Assign node labels
all.nodes <- colnames(p1)
g <- addNode(all.nodes, g)
nodeData(g, all.nodes, attr="label") <- all.nodes

Redrawing the Graph

After setting our node labels, we need to redraw the graph using the redraw function.

# Redraw the graph with updated labels
redraw(rcy)

In this example, rcy is an instance of RCyjs. However, in our original code, we were trying to use rcy without initializing it first.

Correct Sequence

The correct sequence for creating a graph with node labels is:

1. Initialize the default node label.
2. Assign specific labels to each node using nodeData.
3. Redraw the graph using redraw.

Here’s the complete example code:

# Load necessary libraries
library(graph)
library(RCyjs)
library(igraph)

# Read data from file
data <- read.table("text_file_containing_data.txt", sep="\t")

# Create an adjacency matrix
p1 <- cor(data[1:20,1:20], use="p")

# Convert adjacency matrix to graphNEL
g <- igraph.to.graphnel(simplify(graph_from_adjacency_matrix(p1, weighted=T)), directed = TRUE)

# Assign node labels
all.nodes <- colnames(p1)
g <- addNode(all.nodes, g)
nodeDataDefaults(g, attr="label") <- ""
nodeData(g, all.nodes, attr="label") <- all.nodes

# Redraw the graph with updated labels
redraw(rcy)

Conclusion

In this article, we explored how to specify node labels from adjacency matrix columns using RCyjs. We discussed the correct sequence of steps for creating a graph with node labels and provided example code to illustrate the process.

Last modified on 2024-05-07