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Isotopocule coverage

Source: R/plotting.R, R/processing.R
orbi_isotopocule_coverage.Rd

The coverage of each isotopcule across scans/time is an important indicator for data completeness. These functions provide ways to summarize and visualize the isotopocule coverage in a dataset.

Usage

orbi_plot_isotopocule_coverage(
  dataset,
  isotopocules = c(),
  x = c("scan.no", "time.min"),
  x_breaks = NULL,
  n_x_breaks = 5,
  short_time_labels = FALSE,
  add_data_blocks = TRUE,
  colors = c("#7570B3", "#E6AB02", "#66A61E", "#A6761D", "#D95F02", "#1B9E77", "#E7298A",
    "#666666", "#BBBBBB")
)

orbi_get_isotopocule_coverage(dataset)

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"

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").

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.

colors

the fill colors for the isotopocules that carry peak flags, one per flag combination encountered in the data (recycled if there are more combinations than colors). Isotopocules without any flags are always shown in black.

Value

a ggplot object

summary data frame

Functions

  • orbi_plot_isotopocule_coverage(): visualizes isotope coverage. Detected isotopocules are shown by their peak flags - those without any flags in black, those carrying flags in the colors provided. Weak isotopocules (if previously defined by orbi_flag_weak_isotopocules()) are highlighted in red.

  • orbi_get_isotopocule_coverage(): calculates which stretches of the data have data for which isotopocules. This function is usually used indicrectly by orbi_plot_isotopocule_coverage() but can be called directly to investigate isotopocule coverage.