R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 131 found.
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otu_table<- (Package: phyloseq) : Assign a new OTU Table to code{x

Assign a new OTU Table to x

● Data Source: BioConductor
● Keywords:
● Alias: assign-otu_table, otu_table<-, otu_table<-,otu_table,otu_table-method, otu_table<-,phyloseq,otu_table-method, otu_table<-,phyloseq,phyloseq-method
● 0 images

phy_tree<- (Package: phyloseq) : Assign a (new) phylogenetic tree to code{x

Assign a (new) phylogenetic tree to x

● Data Source: BioConductor
● Keywords:
● Alias: assign-phy_tree, phy_tree<-, phy_tree<-,phyloseq,phylo-method, phy_tree<-,phyloseq,phyloseq-method
● 0 images

sample_data<- (Package: phyloseq) : Assign (new) sample_data to code{x

This replaces the current sample_data component of x with value, if value is a sample_data-class. However, if value is a data.frame, then value is first coerced to a sample_data-class, and then assigned. Alternatively, if value is phyloseq-class, then the sample_data component will first be accessed from value and then assigned. This makes possible some concise assignment/replacement statements when adjusting, modifying, or building subsets of experiment-level data. See some examples below.

● Data Source: BioConductor
● Keywords:
● Alias: assign-sample_data, sample_data<-
● 0 images

sample_names<- (Package: phyloseq) : Replace OTU identifier names

Replace OTU identifier names

● Data Source: BioConductor
● Keywords:
● Alias: assign-sample_names, sample_names<-, sample_names<-,ANY,ANY-method, sample_names<-,ANY,character-method, sample_names<-,otu_table,character-method, sample_names<-,phyloseq,character-method, sample_names<-,sample_data,character-method
● 0 images

tax_table<- (Package: phyloseq) : Assign a (new) Taxonomy Table to code{x

Assign a (new) Taxonomy Table to x

● Data Source: BioConductor
● Keywords:
● Alias: assign-tax_table, tax_table<-, tax_table<-,phyloseq,ANY-method, tax_table<-,phyloseq,taxonomyTable-method, tax_table<-,taxonomyTable,ANY-method, tax_table<-,taxonomyTable,taxonomyTable-method
● 0 images

taxa_are_rows<- (Package: phyloseq) : Manually change taxa_are_rows through assignment.

The taxa_are_rows slot is a logical indicating the orientation of the abundance table contained in object x.

● Data Source: BioConductor
● Keywords:
● Alias: assign-taxa_are_rows, taxa_are_rows<-, taxa_are_rows<-,otu_table,logical-method, taxa_are_rows<-,phyloseq,logical-method
● 0 images

taxa_names<- (Package: phyloseq) : Replace OTU identifier names

Replace OTU identifier names

● Data Source: BioConductor
● Keywords:
● Alias: assign-taxa_names, taxa_names<-, taxa_names<-,ANY,ANY-method, taxa_names<-,ANY,character-method, taxa_names<-,XStringSet,character-method, taxa_names<-,otu_table,character-method, taxa_names<-,phylo,character-method, taxa_names<-,phyloseq,character-method, taxa_names<-,taxonomyTable,character-method
● 0 images

build_tax_table (Package: phyloseq) : Build a code{link{tax_table

Build a tax_table from a named possibly-jagged list

● Data Source: BioConductor
● Keywords:
● Alias: build_tax_table
● 0 images

capscale.phyloseq (Package: phyloseq) : Constrained Analysis of Principal Coordinates, code{link[vegan]{capscale

See capscale for details. A formula is main input.

● Data Source: BioConductor
● Keywords: internal
● Alias: capscale.phyloseq, capscale.phyloseq,phyloseq,formula,character-method, capscale.phyloseq,phyloseq,formula,dist-method
● 1 images

cca.phyloseq (Package: phyloseq) : Constrained Correspondence Analysis and Redundancy Analysis.

This is the internal function that simplifies getting phyloseq data into the constrained ordination functions, cca and rda. Unlike capscale.phyloseq, the formula argument to these methods is optional, and results in an unconstrained ordination.

● Data Source: BioConductor
● Keywords: internal
● Alias: cca.phyloseq, cca.phyloseq,otu_table,ANY-method, cca.phyloseq,otu_table-method, cca.phyloseq,phyloseq,NULL-method, cca.phyloseq,phyloseq,formula-method, rda.phyloseq
● 0 images