co_occurence_network: Co-occurence network

In umerijaz/microbiomeSeq: Microbial community analysis in an environmental context.

Description

This function uses co-occurence pattern analysis to identify co-occuring features/taxa in community data under specified environmental conditions. Co-occurence is measured as positive correlation whose threshold(s) can be specified as indicated in arguments section. Amongst these features, pairwise co-occurences which are outstanding within sub communities are detected. p-values generated during pairwise correlations are adjusted for multiple comparisons by false discovery rate. The network statistics used to assign importance of taxa/features include betweenness, closeness, and eigenvector centrality.

Usage

co_occurence_network(physeq, qval_threshold = 0.05, grouping_column,
  rhos = c(-0.75, -0.5, 0.5, 0.75), select.condition = NULL,
  method = "cor", filename = NULL, ...)

Arguments

qval_threshold	Cut off for "fdr" adjusted p-values.
grouping_column	(Required). Character string specifying name of a categorical variable that is preffered for grouping the information. information.
rhos	(required). A vector specifying thresholds for correlation between co-occuring pairs of features.
select.condition	(optional). A character string speifying name of a desired condition/group. If not supplied, co-occuence analysis is performed amongst all conditions present in the grouping variable.
physeq(Required).	A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.
method.	A character string for the correlation method to be used; options include: "cor" and "bicor"

Value

Files of visual representation of the network showing subcommunities (identified by colors), network statistics and file containing pairwise corrrelations of taxa in under different conditions.

Author(s)

Alfred Ssekagiri [e-mail], Umer Zeeshan Ijaz [e-mail]

References

http://userweb.eng.gla.ac.uk/umer.ijaz/, Umer Ijaz, 2015

[Ryan J. Williams, Adina Howe and Kirsten S. Hofmockel. Demonstrating microbial co-occurrence pattern analyses within and between ecosystems, Frontiers in Microbial Ecology, 5:358, 2014].

Examples

data(pitlatrine)
physeq <- taxa_level(pitlatrine, "Phylum")
co_occr <- co_occurence_network(physeq, grouping_column = "Country", rhos = 0.35, select.condition = "V", scale.vertex.size=3, scale.edge.width=15)

umerijaz/microbiomeSeq documentation built on May 30, 2019, 3:13 p.m.