kendrickPlot: Kendrick plot of an ftmsData object

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

Kendrick plot of an ftmsData object

Description

Constructs a Kendrick plot (Kendrick defect vs Kendrick mass) for an object of type ftmsData.

Usage

kendrickPlot(
  ftmsObj,
  title = NA,
  colorPal = NA,
  colorCName = NA,
  vkBoundarySet = "bs1",
  xlabel = "Kendrick Mass",
  ylabel = "Kendrick Defect",
  legendTitle = colorCName,
  base_compound = NULL
)

Arguments

ftmsObj	an object of class 'peakData' or 'compoundData', typically a result of as.peakData or mapPeaksToCompounds.
title	plot title
colorPal	color palette function, one of col_numeric, col_factor or similar scales palette function
colorCName	column name of ftmsObj$e_meta to use for coloring the points. If NA and vkBoundarySet is provided, the points will be colored according to the Van Krevelen category.
vkBoundarySet	character vector specifying which boundary set to use when determining class. Valid options are currently "bs1" and "bs2" and defaults to "bs1". See details of assign_class for differences in sets.
xlabel	x axis label, default is "Kendrick Mass"
ylabel	y axis label, default is "Kendrick Defect"
legendTitle	title for the legend, only used when coloring points according to a numeric scale
base_compound	string specifying the base compound used to calculate the Kendrick Mass you want plotted on the x-axis. Defaults to NULL, in which case the first Kendrick Mass is used.

Value

a plotly object

Author(s)

Amanda White

See Also

plot_ly

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