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 = NULL,
  n_x_breaks = 5,
  short_time_labels = FALSE,
  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,
  use_data_block_names = FALSE,
  show_outliers = TRUE,
  show_points = FALSE,
  point_size = NULL
)

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: which x-axis to use (time vs. scan number). If set to "guess" (the default), the function will try to figure it out from the plot.
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: 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())
use_data_block_names: whether to label the data blocks by their individual block_name (if they have one) instead of just as "data" (the default). This allows color coding the background of the different data blocks (e.g. reference vs. sample). All other blocks (e.g. "unused") are always labeled by their data type.
show_outliers: whether to highlight data previously flagged as outliers by orbi_flag_outliers()
show_points: whether to show the individual data points in addition to the lines connecting them
point_size: the size of the data points (if show_points = TRUE) and of the outlier points (if show_outliers = TRUE). By default (NULL) the ggplot2 default point size is used.

Value

a ggplot object