DatasetDendogram: DatasetDendogram

In nathansam/CircadianTools: Collection of Tools for Detecting Rhythmic Genes

Description

DatasetDendogram

Usage

DatasetDendogram(
  cluster.dataset,
  method = "agglom",
  metric = "euclidean",
  nthreads = NULL,
  print = TRUE,
  save = FALSE,
  path = NULL
)

Arguments

cluster.dataset	A transcriptomics dataset where the final column details the cluster the gene belongs to. First column should be gene names. All remaining columns should be expression levels.
method	The clustering method to be used. Currently accepts 'agglom' and 'diana'.
metric	The distance metric to be used to calculate the distances between genes. See parallelDist::parDist for all accepted arguments. Also allows the option of 'abs.correlation'.
nthreads	Number of processor threads to be used for calculating the distance matrix. If not specified then the maximum number of logical cores is used.
print	Logical. If TRUE renders plot in the plot viewer. Defaults to TRUE
save	Logical. If TRUE, saves plot to working directory. Defaults to FALSE.
path	The directory to be used for saving plots to. Uses the working directory by default. Not used if save = FALSE

Examples

diana.df <- DianaClustering(Laurasmappings, k = 10, nthreads = 2)
DatasetDendogram(diana.df, method = 'diana', nthreads = 2, path = 'example')

nathansam/CircadianTools documentation built on Dec. 26, 2019, 11:30 a.m.