plotting: Plot assignment results

In jasenfinch/MFassign: Molecular Formula Assignment For High Resolution ESI-MS Based Metabolomics Data

Plot assignment results

Description

Plot molecular formula assignment results.

Usage

plotAdductDist(assignment)

## S4 method for signature 'Assignment'
plotAdductDist(assignment)

plotComponent(
  assignment,
  component,
  iteration,
  type = c("selected", "all"),
  label_size = 3,
  axis_offset = 0.1,
  border = NA,
  highlight = NA
)

## S4 method for signature 'Assignment'
plotComponent(
  assignment,
  component,
  iteration,
  type = c("selected", "all"),
  label_size = 3,
  axis_offset = 0.1,
  border = NA,
  highlight = NA
)

plotFeatureComponents(
  assignment,
  feature,
  iteration,
  type = c("all", "selected"),
  max_components = 6,
  label_size = 3,
  axis_offset = 0.1
)

## S4 method for signature 'Assignment'
plotFeatureComponents(
  assignment,
  feature,
  iteration,
  type = c("all", "selected"),
  max_components = 6,
  label_size = 2,
  axis_offset = 0.05
)

plotSpectrum(assignment, MF)

## S4 method for signature 'Assignment'
plotSpectrum(assignment, MF)

Arguments

assignment	an object of S4 class Assignment
component	component number to plot
iteration	the assignment iteration of the component or components
type	the graph type to return. selected returns the assignment graph after component selection. all returns all assignment components.
label_size	node label size
axis_offset	axis proportion by which to increase axis limits. Prevents cut off of node labels.
border	specify a plot border colour
highlight	specify a feature node to highlight
feature	the m/z feature to plot
max_components	themaximum number of components to plot
MF	the assigned molecular formula to plot

Details

• plotComponent - Plot a molecular formula component graph.

• plotFeatureComponents - Plot the possible component graphs for a given feature.

• plotAdductDist - Plot frequency distributions of the assigned adducts.

• plotSpectrum - Plot the spectrum of an assigned molecular formula.

Examples

library(ggraph)
plan(future::sequential)
p <- assignmentParameters('FIE-HRMS')

mf_assignments <- assignMFs(feature_data,p)

## Plot a component
plotComponent(mf_assignments,1,'A&I1')

## Plot the components for a feature
plotFeatureComponents(mf_assignments,'n191.01962','A&I1')

## Plot the adduct distributions
plotAdductDist(mf_assignments)

## Plot the spectrum of an assigned molecular formula
plotSpectrum(mf_assignments,'C6H8O7')

jasenfinch/MFassign documentation built on Feb. 2, 2024, 11:21 a.m.