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 = 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", "#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, 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