neatsort {microbiome} | R Documentation

## Neatmap Sorting

### Description

Sort samples or features based on the neatmap approach.

### Usage

    neatsort(x, target, method = "NMDS", distance = "bray", first = NULL, ...)

### Arguments

`x` | `phyloseq-class` object or a matrix
`target` | For `phyloseq-class` input, the target is either 'sites' (samples) or 'species' (features) (taxa/OTUs); for matrices, the target is 'rows' or 'cols'.
`method` | Ordination method. See `ordinate` from phyloseq package. For matrices, only the NMDS method is available.
`distance` | Distance method. See `ordinate` from phyloseq package.
`first` | Optionally provide the name of the first sample/taxon to start the ordering (the ordering is cyclic so we can start at any point). The choice of the first sample may somewhat affect the overall ordering.
`...` | Arguments to be passed.

### Details

This function borrows elements from the heatmap implementation in the phyloseq package. The row/column sorting is there not available as a separate function at present, however, hindering reuse in other tools. Implemented in the microbiome package to provide an independent method for easy sample/taxon reordering for phyloseq objects.

### Value

Vector of ordered elements

### References

This function is partially based on code derived from the phyloseq package. For the original neatmap approach for heatmap sorting, see (and cite): Rajaram, S., & Oono, Y. (2010). NeatMap–non-clustering heat map alternatives in R. BMC Bioinformatics, 11, 45.

### Examples

    data(peerj32)
    pseq <- peerj32$phyloseq
    # For Phyloseq
    sort.otu <- neatsort(pseq, target='species')
    # For matrix
    # sort.rows <- neatsort(abundances(pseq), target='rows')

[Package microbiome version 1.12.0 Index]