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)
. By default includes all isotopcules that have not been previously identified by orbi_flag_weak_isotopcules()
(if already called on dataset). To narrow down the isotopocules to show, use the isotopocule
parameter.
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"),
color_scale = scale_color_manual(values = colors),
add_data_blocks = TRUE,
add_all_blocks = FALSE,
show_outliers = TRUE
)
Arguments
- dataset
isox dataset
- 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"
- 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 oneisotopocules
as this is identical for different istopocules),ratio
. Depending on the variable, you may want to adjust they_scale
and potentiallyy_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, setadd_data_blocks = FALSE
and manually call theorbi_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 inorbi_add_blocks_to_plot()
)- show_outliers
whether to highlight data previously flagged as outliers by
orbi_flag_outliers()