plotSOI

Source: R/Plot_functions.R

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.

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

# S4 method for 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

See also

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

Author

Roger Gine

Examples

struct <- readRDS(system.file("extdata", "exampleObject.rds",
                             package = "RHermes"))
p <- plotSOI(struct, 1, "C5H11NO2", c("M+H", "M+Na", "M+K"), c(80, 120))