visualize_gene_network: Gene-gene network visualization

Description Usage Arguments

View source: R/visualize_network.R

Description

Builds and visualizes an ADAGE-derived gene-gene network of genes in the selected signatures. In the network, each node represents a gene and two nodes are linked by an edge if the correlation of the two connected genes in the ADAGE model is higher than a certain cutoff. Edge width denotes the correlation strength and edge color indicates positive (purple) or negative (green) correlation. If a value associated with the expression of each gene in a dataset (such as fold change or correlation to phenotype) is provided, it will be used to color gene nodes in the network with red meaning high positive value and blue meaning high negative value. If curated pathways such as KEGG pathways are provided, they will be used to annotate genes in the network and color the node border. Genes that have been annotated by curated pathways are colored black and others grey.

Usage

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visualize_gene_network(selected_signatures, model, cor_cutoff = 0.5,
  gene_color_value = NULL, curated_pathways = NULL, random_seed = 123)

Arguments

selected_signatures

a vector storing names of signatures. Genes in them will be included in the gene-gene network.

model

an ADAGE model to build gene-gene network from

cor_cutoff

numeric, the correlation cutoff to decide whether an edge between two genes exists in the network (default: 0.5).

gene_color_value

a data.frame with two columns, one is geneID, the other could be logFC, correlation, or other value associated with each gene. This value will be used to color genes in the network. If not provided, the gene color in the gene-gene network is uniformly blue. (default: NULL).

curated_pathways

a named list with each element being a gene set, such as the output of the function fetch_geneset(). (default: NULL).

random_seed

int, control the layout of the network. The layout will be the same if the same random_seed is provided (default: 123).


greenelab/ADAGEpath documentation built on Sept. 24, 2017, 2:35 a.m.