romicsHclust: romicsHclust()

In PNNL-Comp-Mass-Spec/RomicsProcessor: omics-oriented package for reproducible and sharable data processing pipelines

romicsHclust()

Description

Plots the hierarchical clustering of the samples contaned in the romics_object calculated using the functions dist() and hclust() (see documentation of those R functions for more details). The colors used for the plotting will correspond to the main_factor of the romics_object.

Usage

romicsHclust(
  romics_object,
  method_dist = "euclidean",
  method_hclust = "ward.D"
)

Arguments

romics_object	has to be a log transformed romics_object created using romicsCreateObject() and transformed using the function log2transform() or log10transform()
method_dist	the distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Any unambiguous substring can be given.
method_hclust	the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).

Details

This function uses the dist() and hclust() functions to calculate the hierachical clustering and then plots the hclust with colors based on the current main_factor of the romics_object.

Value

a hierarchical clustering tree plot with its branches colored by factor.

Author(s)

Geremy Clair

PNNL-Comp-Mass-Spec/RomicsProcessor documentation built on March 18, 2023, 5:14 a.m.