MDSPlot: MDSPlot

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

Description

Applies multidimensional scaling to a clustered transcriptomics dataset to reduce the clusters to two dimensions and then plots the clusters.

Usage

MDSPlot(
  cluster.dataset,
  title = "Multidimensional Scaling Plot",
  nthreads = NULL,
  metric = "euclidean",
  save = FALSE,
  print = TRUE
)

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.
title	The title to be used in the plot
nthreads	Number of processor threads for the process. If not specified then the maximum number of logical cores are used.
metric	The distance metric to be used to calculate the distances between genes. See parallelDist::parDist for all accepted arguments. Also accepts "abs.correlation" for absolute Pearson's correlation
save	Logical. If TRUE, saves plots. Defaults to FALSE.
print	Logical. If TRUE renders significant genes in the plot viewer. Defaults to TRUE

Examples

cluster.df <- PamClustering(Laurasmappings, k = 10, scale = TRUE,
                            nthreads = 2)
MDSPlot(cluster.df, nthreads = 2)

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