Visualize data — orbi_plot_raw

Call this function to visualize orbitrap data vs. time or scan number. The most common uses are orbi_plot_raw_data(y = intensity), orbi_plot_raw_data(y = ratio), and orbi_plot_raw_data(y = tic * it.ms). If the selected y is peak-specific data (rather than scan-specific data like tic * it.ms), the isotopocules argument can be used to narrow down which isotopocules will be plotted. By default includes all isotopcules that have not been previously identified by orbi_flag_weak_isotopcules() (if already called on dataset).

Usage

orbi_plot_raw_data(
  dataset,
  isotopocules = c(),
  x = c("time.min", "scan.no"),
  x_breaks = scales::breaks_pretty(5),
  y,
  y_scale = c("raw", "linear", "pseudo-log", "log"),
  y_scale_sci_labels = TRUE,
  color = .data$isotopocule,
  colors = c("#1B9E77", "#D95F02", "#7570B3", "#E7298A", "#66A61E", "#E6AB02", "#A6761D",
    "#666666", "#BBBBBB"),
  color_scale = scale_color_manual(values = colors),
  add_data_blocks = TRUE,
  add_all_blocks = FALSE,
  show_outliers = TRUE
)

Arguments

dataset: An aggregated dataset or a data frame of peaks (i.e. works directly after orbi_identify_isotopocules() as well as with a tibble from orbi_get_data(peaks = everything()) or when reading from an IsoX file)
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"
x_breaks: what breaks to use for the x axis, change to make more specifid tickmarks
y: expression for what to plot on the y-axis, e.g. intensity, tic * it.ms (pick one isotopocules as this is identical for different istopocules), ratio. Depending on the variable, you may want to adjust the y_scale and potentially y_scale_sci_labels argument.
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
color: expression for what to use for the color aesthetic, default is isotopocule
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
add_data_blocks: add highlight for data blocks if there are any block definitions in the dataset (uses orbi_add_blocks_to_plot()). To add blocks manually, set add_data_blocks = FALSE and manually call the orbi_add_blocks_to_plot() function afterwards.
add_all_blocks: add highlight for all blocks, not just data blocks (equivalent to the data_only = FALSE argument in orbi_add_blocks_to_plot())
show_outliers: whether to highlight data previously flagged as outliers by orbi_flag_outliers()

Value

a ggplot object