plot.mdsSim: View patient clusters using multi-dimensional scaling.

In BRL-BCM/CTDext: Extension package for the CTD R package.

View patient clusters using multi-dimensional scaling.

Description

This function plots the provided patient similarity matrix in a lower dimensional space using multi-dimensional scaling, which is well suited for similarity metrics.

Usage

plot.mdsSim(patientSim, diagnoses, k, diag)

Arguments

patientSim	- The patient similarity matrix.
diagnoses	- A character vector of diagnostic labels associated with the rownames of patientSim.
k	- The number of dimension you want to plot your data using multi-dimensional scaling.
diag	- The diagnosis associated with positive controls in your data.

Value

p - a plotly scatter plot colored by provided diagnostic labels.

Examples

# if you have diagnostic labels associated with the colnames(data_mx), send them using diagnoses parameter
p = plot.mdsSim(patientSim, diagnoses, k=2, diag="diseased")
p
p = plot.mdsSim(patientSim, diagnoses, k=3, diag="diseased")
p

BRL-BCM/CTDext documentation built on May 7, 2022, 5:31 a.m.