dtnetplot: Drug-Target Network Visualization

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Drug-Target Network Visualization

Description

Functional modules of GESS and FEA results can be rendered as interactive drug-target networks using the dtnetplot function form signatureSearch. For this, a character vector of drug names along with an identifier of a chosen functional category are passed on to the drugs and set arguments, respectively. The resulting plot depicts the corresponding drug-target interaction network. Its interactive features allow the user to zoom in and out of the network, and to select network components in the drop-down menu located in the upper left corner of the plot.

Usage

dtnetplot(drugs, set, ont = NULL, desc = NULL, verbose = FALSE, ...)

Arguments

drugs	A character vector of drug names
set	character(1) GO term ID, KEGG or Reactome pathway ID. Alternatively, a character vector of gene SYMBOLs can be assigned.
ont	if 'set' is a GO term ID, 'ont' is the corresponding ontology that GO term belongs to. One of 'BP', 'MF' or 'CC'. If 'set' is anything else, 'ont' is ignored.
desc	character(1), description of the chosen functional category or target set
verbose	TRUE or FALSE, whether to print messages
...	Other arguments passed on to visNetwork function.

Value

visNetwork plot and a list of drugs and targets that have interactions

Examples

data(drugs10)
dtnetplot(drugs=drugs10, 
    set=c("HDAC1", "HDAC2", "HDAC3", "HDAC11", "FOX2"),
    desc="NAD-dependent histone deacetylase activity (H3-K14 specific)")

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.