constructFullNetwork: Build A Full Simple Sugar Degradation Network For One Genome

In MolyWang/microCompet: Identify A Microbe's Potential Nutrition Competitor From Microbiota

Build A Full Simple Sugar Degradation Network For One Genome

Description

Given a name of a microbe, a vector of gene names for sugar degradation enzymes, and a data.frame containing all enzymatic reactions of interest, this function constructs a network plot that represents all sugar degradation steps the given microbe/genome can perform.

Usage

constructFullNetwork(genomeName, geneVec, ER)

Arguments

genomeName	Name of the microbe to be plotted.
geneVec	A vector containing gene names of all sugar degradation enzymes present in the given microbial genome (genomeName).
ER	A data.frame containing all enzymatic reactions of interest, and should represent enzymatic reactions with at least four characteristics: Gene, Substrate, Product, Sugar. Header should be EXACTLY the same. (See the sample dataset EnzymaticReactions for example by ?EnzymaticReactions). Rows containing NA will be removed.

Details

In the output plot, one vertex represents one compound, and its size suggests the number of sugar degradation pathways it involves in. You can interpret vertex size as the importance of a compound within this network.

Similarly, one edge represents one enzymatic reaction that convert the tail vertex (a reaction substrate) to the head vertex (a reaction product). Thickness of one edge represents number of genes that encoding enzymes capable of catalyzing this reaction, and represents the robustness of this step.

Color of the edge represents the sugar degradation pathway this step involved in.

Value

A network graph representing the full simple sugar degradation pathway of the genome given as geneVec.

Examples

## Not run: 
 require("microCompet")
 ER <- microCompet::EnzymaticReactions
 ED <- microCompet::EnzymeDistribution
 fullEnzymeGeneVec <- ED$Gene
 genomeFilePath <- system.file("extdata",
                               "Lactobacillus_johnsonii.gb",
                               package = "microCompet",
                               mustWork = TRUE)
 carboGenes <- extractCarboGenes(genomeFilePath, fullEnzymeGeneVec)
 fullNetwork <- constructFullNetwork("Lactobacillus_johnsonii", carboGenes, ER)
 fullNetwork

## End(Not run)

MolyWang/microCompet documentation built on Feb. 26, 2023, 9:29 p.m.