QuantilePlots: QuantilePlots

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

Description

Finds the quartiles for intercluster distances and plots these distances as a set of histograms

Usage

QuantilePlots(
  cluster.dataset,
  metric = "euclidean",
  nthreads = NULL,
  save = TRUE,
  print = TRUE,
  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.
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 for the process. If not specifed then the maximum number of logical cores are used.
save	Logical. If TRUE, saves the histogram plots to working directory. Defaults to FALSE.
print	Logical. If TRUE renders the histogram plots in the plot viewer. Defaults to TRUE
path	The directory to be used for saving plots to. Uses the working directory by default. Not used if save=FALSE

Examples

pam <- PamClustering(Laurasmappings, k = 10, nthreads = 2)
QuantilePlots(pam, path='Pam_Anova_Distance_Histograms', nthreads = 2)

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