compAgree: Comparison of agreement between two subtypes

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

Compute the Rand Index, Jaccard Index, Fowlkes-Mallows, and Normalized Mutual Information for agreement of two partitions, and generate alluvial diagrams for visualization.

Usage

compAgree(
  moic.res = NULL,
  subt2comp = NULL,
  doPlot = TRUE,
  clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627",
    "#023E8A", "#9D4EDD"),
  box.width = 0.1,
  fig.name = NULL,
  fig.path = getwd(),
  width = 6,
  height = 5
)

Arguments

moic.res	An object returned by 'getMOIC()' with one specified algorithm or 'get%algorithm_name%' or 'getConsensusMOIC()' with a list of multiple algorithms.
subt2comp	A data.frame of subtypes that need to compare with current subtype with rownames for samples and columns for other subtypes.
doPlot	A logic value to indicate if generating alluvial diagram to show the agreement of different subtypes; TRUE by default.
clust.col	A string vector storing colors for each cluster.
box.width	A numeric valur to indicate the width for box in alluvial diagram.
fig.name	A string value to indicate the name of the figure.
fig.path	A string value to indicate the output path for storing the figure.
width	A numeric value to indicate the width of alluvial diagram.
height	A numeric value to indicate the height of alluvial diagram.

Value

A figure of agreement (.pdf) if doPlot = TRUE and a data.frame storing four agreement measurements, including Rand Index (RI), Adjusted Mutual Information (AMI), Jaccard Index (JI), and Fowlkes-Mallows (FM).

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.