orbi_plot_satellite_peaks: Visualize satellite peaks

In isoverse/isoorbi: Process Orbitrap Isotopocule Data

Visualize satellite peaks

Description

Call this function any time after flagging the satellite peaks to see where they are. Use the isotopocules argument to focus on the specific isotopocules of interest.

Usage

orbi_plot_satellite_peaks(
  dataset,
  isotopocules = c(),
  x = c("scan.no", "time.min"),
  x_breaks = scales::breaks_pretty(5),
  y_scale = c("log", "pseudo-log", "linear", "raw"),
  y_scale_sci_labels = TRUE,
  colors = c("#1B9E77", "#D95F02", "#7570B3", "#E7298A", "#66A61E", "#E6AB02", "#A6761D",
    "#666666"),
  color_scale = scale_color_manual(values = colors)
)

Arguments

dataset	isox dataset with satellite peaks identified (orbi_flag_satellite_peaks())
isotopocules	which isotopocules to visualize, if none provided will visualize all (this may take a long time or even crash your R session if there are too many isotopocules in the data set)
x	x-axis column for the plot, either "time.min" or "scan.no"
x_breaks	what breaks to use for the x axis, change to make more specifid tickmarks
y_scale	what type of y scale to use: "log" scale, "pseudo-log" scale (smoothly transitions to linear scale around 0), "linear" scale, or "raw" (if you want to add a y scale to the plot manually instead)
y_scale_sci_labels	whether to render numbers with scientific exponential notation
colors	which colors to use, by default a color-blind friendly color palettes (RColorBrewer, dark2)
color_scale	use this parameter to replace the entire color scale rather than just the colors

Value

a ggplot object

isoverse/isoorbi documentation built on Aug. 9, 2024, 3:42 p.m.