Plot assignment results — plotAdductDist • assignments

Plot molecular formula assignment results.

Usage

plotAdductDist(assignment)

# S4 method for 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 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 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 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)
#> Loading required package: ggplot2
plan(future::sequential)
p <- assignmentParameters('FIE-HRMS')

mf_assignments <- assignMFs(feature_data,p)
#> 
#> assignments v1.0.2 Thu Jan 11 15:07:35 2024
#> ________________________________________________________________________________
#> Assignment Parameters: 
#> 
#> 	 Technique:		 FIE-HRMS 
#> 	 Max M:			 800 
#> 	 MF rank threshold:	 3 
#> 	 PPM threshold:		 4 
#> 	 Relationship limit:	 0.001 
#> 	 RT limit:		  
#> 	 Correlations:
#> 		method: spearman
#>  		pAdjustMethod: bonferroni
#>  		corPvalue: 0.05
#>  		minCoef: 0.7
#>  		maxCor: Inf
#> 
#> 	 Adducts: 
#> 	 n: [M-H]1-, [M+Cl]1-, [M+Cl37]1-, [M+K-2H]1-, [M-2H]2-, [2M-H]1-
#> 	 p: [M+H]1+, [M+K]1+, [M+Na]1+, [M+K41]1+, [M+2H]2+, [2M+H]1+ 
#> 	 Isotopes: 13C, 18O 
#> 	 Transformations: M - [O] + [NH2], M - [OH] + [NH2], M + [H2], M - [H2] + [O], M - [H] + [CH3], M - [H] + [NH2], M - [H] + [OH], M + [H2O], M - [H3] + [H2O], M - [H] + [CHO2], M - [H] + [SO3], M - [H] + [PO3H2]
#> ________________________________________________________________________________
#> No. m/z:	10
#> Calculating correlations …

#> Calculating correlations 	✔ [10 correlations] [0.2S]
#> Calculating relationships …

#> Calculating relationships 	✔ [1.5S]
#> Adduct & isotopic assignment …
#> generating molecular formulas…

#> generating molecular formulas	✔ [8.5S]
#> iteration 1…

#> iteration 1			✔ [0.4S]
#> iteration 2…

#> Adduct & isotopic assignment 	✔ [9.6S]
#> Transformation assignment…
#> iteration 1 …

#> iteration 1 			✔ [1.2S]
#> iteration 2 …

#> Transformation assignment 	✔ [1.2S]
#> ________________________________________________________________________________
#> 
#> Complete! [12.7S]

## 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')