Visualize satellite peaks — orbi_plot_satellite

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"),
  y = c("ions.incremental", "intensity"),
  x_breaks = NULL,
  n_x_breaks = 5,
  short_time_labels = FALSE,
  y_scale = c("log", "pseudo-log", "linear", "raw"),
  y_scale_sci_labels = TRUE,
  colors = c("#1B9E77", "#D95F02", "#7570B3", "#E7298A", "#66A61E", "#E6AB02", "#A6761D",
    "#666666", "#BBBBBB"),
  color_scale = scale_color_manual(values = colors)
)

Arguments

dataset: a data frame or aggregated dataset with satellite peaks already identified (i.e. after 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", default is "scan.no"
y: y-axis column for the plot, typially either "ions.incremental" or "intensity", default is "ions.incremental" (falls back to "intensity" if "ions.incremental" has not been calculated yet for the provided dataset)
x_breaks: what breaks to use for the x axis. By default (NULL) these are pretty breaks for scan numbers or pretty time intervals for time (which is labeled as a duration, e.g. 1:30 min), provide breaks to make more specific tickmarks. Use either x_breaks or n_x_breaks, not both.
n_x_breaks: the desired number of x axis breaks when using the default pretty breaks (x_breaks = NULL), default: 5. Use either x_breaks or n_x_breaks, not both.
short_time_labels: whether to use compact time axis labels with no space between value and unit and abbreviated units (hr, m, s), e.g. 1:30m instead of 1:30 min. Only relevant for a time based x axis (x = "time.min").
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