plotPrincipalCoordinates: Plot principal coordinates of ftmsData samples

In EMSL-Computing/fticRanalysis: Analysis and visualization tools for FT-MS data

Plot principal coordinates of ftmsData samples

Description

Constructs a scatter plot of any combination of principal coordinates calculated by the getPrincipalCoordinates function. If an associated ftmsData object is provided with groups defined, the resulting plot will be colored by group membership.

Usage

plotPrincipalCoordinates(
  pcoaMat,
  x = 1,
  y = 2,
  ftmsObj = NA,
  title = NA,
  xlabel = sprintf("Principal Coordinate %d", x),
  ylabel = sprintf("Principal Coordinate %d", y),
  includeR2OnAxes = TRUE,
  size = 8
)

Arguments

pcoaMat	numeric matrix, the output of getPrincipalCoordinates
x	numeric value, which column of pcoaMat should serve as the x-axis
y	numeric value, which column of pcoaMat should serve as the y-axis
ftmsObj	optional, if provided points will be colored according to the groups defined in ftmsObj
title	optional plot title
xlabel	x-axis label
ylabel	y-axis label
includeR2OnAxes	TRUE/FALSE, should the x- and y-axis labels be appended with R^2 values?
size	plot marker size (default is 8)

Value

a plotly plot object

Examples

## Not run: 
pcoaMat <- getPrincipalCoordinates(exampleProcessedPeakData)
plotPrincipalCoordinates(pcoaMat, x=2, y=3, ftmsObj=exampleProcessedPeakData)

## End(Not run)

EMSL-Computing/fticRanalysis documentation built on Dec. 18, 2024, 9:51 p.m.