Compute_similarities: Compute similarities for Net-SNE or BhtSNE.

In schwikowskilab/rNetSNE: Run Net-SNE on R

Description

Compute similarities for Net-SNE or BhtSNE.
Input : cell/variable matrix saved as binary file (.dat) with Write_binary_file.
Output : binary file (.dat) used for RunBhtSNE or RunNetSNE.
Requirment: C++ implementation of Net-SNE installed and functional.

Usage

Compute_similarities(perp = 30L, verbose = TRUE,
                     path.netSNE.dir = path.netSNE.dir,
                     path.to.bin.file = path.to.bin.file,
                     path.output.file)

Arguments

perp	Integer; Stands for 'Perplexity', an integer between 0 and 100 (see t-SNE documentation, default: 30)
verbose	Logical; Should the outputs be printed to the console? (default: TRUE)
path.netSNE.dir	Character; The path to the directory containing the executables created after Net-SNE installation (usually : path/to/netsne-master/bin). Must end with the name of directory with exectuables (here: '/bin')
path.to.bin.file	Character; The path to the binary file of the train data matrix obtained with Write_binary_file
path.output.file	Character; The path to save the output file (see Details)

Details

The path to the Net-SNE directory (path.netSNE.dir) must end with the directory containing the executables (ComputeP in this case). Therefore, it should end with "bin" (no slash after bin).

The path to the save the output directory (path.output.dir) must be of the form "Documents/MyProject/SimFile.dat". "Documents/MyProject" must exist, while "SimFile.dat" is the name of the file to be created and thefore should not exist.

Value

The function does not return anything but creates a binary file to the path specified with path.output.dir.

Examples

data(iris)
labels = iris[,5]
iris = iris[,1:4]

path.netSNE.dir = "~/netsne-master/bin"
path.output
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schwikowskilab/rNetSNE documentation built on May 4, 2019, 6:40 p.m.