Package index • ramen

All functions

ConsortiumMetabolism(): Functional Microbiome Representation
ConsortiumMetabolismAlignment() as.data.frame(<ConsortiumMetabolismAlignment>): Constructor for ConsortiumMetabolismAlignment Objects
ConsortiumMetabolismSet(): Set of ConsortiumMetabolism Objects
align(): Align Consortium Metabolisms
as.data.frame(<ConsortiumMetabolism>): Coerce a ConsortiumMetabolism to a data.frame
as.data.frame(<ConsortiumMetabolismSet>): Coerce a ConsortiumMetabolismSet to a data.frame
compareSpecies(): Compare Two Species by Pathway Set
consortia(): Get the Constituent Consortia
description() `description<-`(): Get or Set Object Description
extractCluster(): Extract a Cluster
filterConsortia(): Filter Consortia from a Set
functionalGroups(): Get Functional Groups
growth(): Get Growth Rates
importMisosoup(): Import MiSoSoup YAML Output
importSmetana(): Import SMETANA Detailed Output
metabolites(): Get Metabolites
misosoup24: Example Data from MiSoSoup 2024
name() `name<-`(): Get or Set Object Name
overlapMatrix(): Get Overlap Matrix
pathways(): Retrieve Metabolic Pathways
pivotCM(): Pivot ConsortiumMetabolism Input Data
plot(<ConsortiumMetabolism>,<ANY>): Plot a ConsortiumMetabolism object
plot(<ConsortiumMetabolismAlignment>,<ANY>): Plot a ConsortiumMetabolismAlignment object
plot(<ConsortiumMetabolismSet>,<ANY>): Plot a ConsortiumMetabolismSet object
plotDirectedFlow(): Plot a Directed Graph Emphasising Flow
plotFunctionalGroups(): Plot Functional Groups Dendrogram
prevalence(): Get Pathway Prevalence
ramenPalette: Ramen package palette
scores(): Get Alignment Scores
show(<ConsortiumMetabolism>): Show Method for ConsortiumMetabolism Object
show(<ConsortiumMetabolismAlignment>): Show method for ConsortiumMetabolismAlignment Objects
show(<ConsortiumMetabolismSet>): Show Method for ConsortiumMetabolismSet Object
similarityMatrix(): Get Similarity Matrix
species(): Return Species in a Consortium
speciesSummary(): Species Summary
`[`(<ConsortiumMetabolism>,<ANY>,<ANY>,<ANY>) `[`(<ConsortiumMetabolismSet>,<ANY>,<ANY>,<ANY>) `[`(<ConsortiumMetabolismAlignment>,<ANY>,<ANY>,<ANY>): Subset ramen Objects by Metabolite
synCM(): Generate Synthetic Consortium Metabolism
theme_ramen(): Ramen plot theme