Cyclogram: Comparison of clustering results over multiple results in...

In MosaiClusteR: An Umbrella Framework for Multi-Source and Multi-Omics Clustering

Comparison of clustering results over multiple results in circular format

Description

A visual comparison of all methods is handy to see which objects will always cluster together independent of the applied methods. To this aid the function Cyclogram has been written. The function relies on methods of the circlize package.

Usage

Cyclogram(
  List,
  nrclusters = NULL,
  cols = NULL,
  fusionsLog = FALSE,
  weightclust = FALSE,
  names = NULL,
  canvaslims = c(-1, 1, -1, 1),
  margins = c(8.1, 3.1, 3.1, 4.1),
  Highlight = NULL,
  cex.highlight = 1,
  substr = NULL,
  cex.labels = 0.9,
  plottype = "new",
  location = NULL
)

Arguments

List	A list of the outputs from the methods to be compared. The first element of the list will be used as the reference in ReorderToReference.
nrclusters	The number of clusters to cut the dendrogram in. Default is NULL.
cols	A character vector with the colours to be used. Default is NULL.
fusionsLog	Logical. To be handed to ReorderToReference: indicator for the fusion of clusters. Default is TRUE
weightclust	Logical. To be handed to ReorderToReference: to be used for the outputs of CEC, WeightedClust or WeightedSimClust. If TRUE, only the result of the Clust element is considered. Default is TRUE.
names	Optional. Names of the methods to be used as labels for the columns. Default is NULL.
canvaslims	The limits for the circular dendrogam. Default is c(-1.0,1.0,-1.0,1.0).
margins	Optional. Margins to be used for the plot. Default is c(8.1,3.1,3.1,4.1).
Highlight	Optional. A list of character vectors of objects to be highlighted. Default is NULL.
cex.highlight	Magnification for the highlight text. Default is 1.
substr	Optional. A vector of length two giving start and stop positions to shorten labels. Default is NULL.
cex.labels	Magnification for the labels. Default is 0.7.
plottype	Should be one of "pdf","new" or "sweave". If "pdf", a location should be provided in "location" and the figure is saved there. If "new" a new graphic device is opened and if "sweave", the figure is made compatible to appear in a sweave or knitr document, i.e. no new device is opened and the plot appears in the current device or document. Default is "new".
location	Optional. If plottype is "pdf", a location should be provided in "location" and the figure is saved there. Default is NULL.

Details

This function makes use of the functions ReorderToReference and Colorsnames. Given a list with the outputs of several methods, the first step is to call upon ReorderToReference and to produce a matrix of which the columns are ordered according to the ordering of the objects of the first method in the list. Each cell represent the number of the cluster the object belongs to for a specific method indicated by the rows. The clusters are arranged in such a way that these correspond to that one cluster of the referenced method that they have the most in common with. The circlize package is used to visualize the matrix is a circular format. The inner element of the circle is the first element of the List parameter, the second inner element is the second element of the list and so on. The object names are written on the circular dendrogram portayed in the center of the circle.

Value

A plot which translates the matrix output of the function ReorderToReference into a circular format.

MosaiClusteR documentation built on Oct. 25, 2026, 1:08 a.m.