plotSOI: plotSOI

In RogerGinBer/RHermes: Improving metabolome characterization using molecular formula databases

plotSOI

Description

Plots the SOI data points, the non-SOI points with the same annotation and, if blank subtraction was performed, it also plots the blank data points.

Usage

plotSOI(
  struct,
  id,
  formula,
  ads = NA,
  rtrange = c(0, 10000),
  dynamicaxis = TRUE,
  interactive = TRUE
)

## S4 method for signature 'RHermesExp,numeric,character'
plotSOI(
  struct,
  id,
  formula,
  ads = NA,
  rtrange = c(0, 10000),
  dynamicaxis = TRUE,
  interactive = TRUE
)

Arguments

struct	An RHermesExp object
id	Number of the SOI list to plot
formula	Formula annotation to search for (eg. "C6H12O6")
ads	Adducts to plot. Defaults to NA, which plots all of them by default.
rtrange	The retention time interval to plot, in seconds (eg. c(0,1000)). Defaults to a 0-10000s interval, which will cover all points.
dynamicaxis	Whether to use a fixed y scale for all adducts or to adapt the scale according to each adduct intensity
interactive	Whether to return a plotly object or a ggplot. Defaults to TRUE (plotly).

Value

An interactive plot_ly object or a static ggplot, depending on the value of interactive

Author(s)

Roger Gine

See Also

Other plots: plotFidelity(), plotRawMS2(), plotSS()

Examples

p <- plotSOI(struct, 1, "C5H11NO2", c("M+H", "M+Na", "M+K"), c(80, 120))

RogerGinBer/RHermes documentation built on April 5, 2025, 10:16 a.m.