plot_network: Plot network

In almeidasilvaf/syntenet: Inference And Analysis Of Synteny Networks

Plot network

Description

Plot network

Usage

plot_network(
  network = NULL,
  clusters = NULL,
  cluster_id = NULL,
  color_by = "cluster",
  interactive = FALSE,
  dim_interactive = c(600, 600)
)

Arguments

network	The synteny network represented as an edge list, which is a 2-column data frame with each member of the anchor pair in a column.
clusters	A 2-column data frame with the variables Gene and Cluster representing gene ID and cluster ID, respectively, exactly as returned by cluster_network.
cluster_id	Character scalar or vector with cluster ID. If more than one cluster is passed as input, clusters are colored differently.
color_by	Either "cluster" or a 2-column data frame with gene IDs in the first column and variable to be used for coloring (e.g., taxonomic information) in the second column.
interactive	Logical scalar indicating whether to display an interactive network or not. Default: FALSE.
dim_interactive	Numeric vector of length 2 with the window dimensions of the interactive plot. If interactive is set to FALSE, this parameter is ignored.

Value

A ggplot object with the network.

Examples

data(network)
data(clusters)
# Option 1: 1 cluster
cluster_id <- 25
plot_network(network, clusters, cluster_id)

# Option 2: 2 clusters
cluster_id <- c(25, 1089)
plot_network(network, clusters, cluster_id)

# Option 3: custom annotation for coloring
species_order <- c(
    "vra", "van", "pvu", "gma", "cca", "tpr", "mtr", "adu", "lja",
    "Lang", "car", "pmu", "ppe", "pbr", "mdo", "roc", "fve",
    "Mnot", "Zjuj", "jcu", "mes", "rco", "lus", "ptr"
) 
species_annotation <- data.frame(
   Species = species_order,
   Family = c(rep("Fabaceae", 11), rep("Rosaceae", 6),
              "Moraceae", "Ramnaceae", rep("Euphorbiaceae", 3), 
              "Linaceae", "Salicaceae")
)
genes <- unique(c(network$node1, network$node2))
gene_df <- data.frame(
    Gene = genes,
    Species = unlist(lapply(strsplit(genes, "_"), head, 1))
)
gene_df <- merge(gene_df, species_annotation)[, c("Gene", "Family")]

plot_network(network, clusters, cluster_id = 25, color_by = gene_df)

almeidasilvaf/syntenet documentation built on Oct. 12, 2024, 5:51 p.m.