Rphenograph {CytoTree} | R Documentation

## RphenoGraph clustering

### Description

R implementation of the PhenoGraph algorithm

A simple R implementation of the [PhenoGraph](http://www.cell.com/cell/abstract/S0092-8674(15)00637-6) algorithm, which is a clustering method designed for high-dimensional single-cell data analysis. It works by creating a graph ("network") representing phenotypic similarities between cells by calclating the Jaccard coefficient between nearest-neighbor sets, and then identifying communities using the well known [Louvain method](https://sites.google.com/site/findcommunities/) in this graph.

This function is developed by Hao Chen and updated by Yuting Dai.

### Usage

    Rphenograph(data, k = 30)

### Arguments

`data` | matrix; input data matrix
`k` | integer; number of nearest neighbours (default:30)

### Value

a list contains an igraph graph object for `graph_from_data_frame` and a communities object, the operations of this class contains:

`print` | returns the communities object itself, invisibly.
`length` | returns an integer scalar.
`sizes` | returns a numeric vector.
`membership` | returns a numeric vector, one number for each vertex in the graph that was the input of the community detection.
`modularity` | returns a numeric scalar.
`algorithm` | returns a character scalar.
`crossing` | returns a logical vector.
`is_hierarchical` | returns a logical scalar.
`merges` | returns a two-column numeric matrix.
`cut_at` | returns a numeric vector, the membership vector of the vertices.
`as.dendrogram` | returns a dendrogram object.
`show_trace` | returns a character vector.
`code_len` | returns a numeric scalar for communities found with the InfoMAP method and NULL for other methods.
`plot` | for communities objects returns NULL, invisibly.

cluster information

### Author(s)

Hao Chen <chen_hao@immunol.a-star.edu.sg>

### References

Jacob H. Levine and et.al. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell, 2015.

### Examples

    iris_unique <- unique(iris) # Remove duplicates
    data <- as.matrix(iris_unique[, seq_len(4)])
    Rphenograph_out <- Rphenograph(data, k = 45)
    modularity(Rphenograph_out[[2]])
    membership(Rphenograph_out[[2]])
    iris_unique$phenograph_cluster <- factor(membership(Rphenograph_out[[2]]))

[Package CytoTree version 1.4.0 Index]