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Uncertainty of the peptide measurements

plot_uncertainty.Rd

Plot the uncertainty of the mass measurements - for aggregated data or before aggregation - to see if there is a region with uncertainty higher than acceptable

Usage

plot_uncertainty(
  dat,
  protein = dat[["Protein"]][1],
  state = dat[["State"]][1],
  skip_amino = 0,
  aggregated = TRUE,
  separate_times = TRUE,
  show_threshold = TRUE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

dat

data imported by the read_hdx function

protein

selected protein

state

selected biological state for given protein

skip_amino

integer, indicator how many aminos from the N-terminus should be omitted

aggregated

logical, indicator if presented data is aggregated on replicate level

separate_times

logical, indicator if the values for different time points are presented separately

show_threshold

logical, indicator if the threshold of significance is shown

interactive

...

Value

a ggplot object

Details

The function plot_uncertainty generates a plot of uncertainty of mass measurement of each peptide from selected protein in selected biological state. The values can be presented in two ways: as aggregated values for each replicate, or before aggregation - measured values for charge values within a replicate. On X-axis there is a position in a sequence, with length of a segment of each peptide representing its length. On Y-axis there is uncertainty of the measurement in Daltons. The threshold is set to 1 Da, as this value is associated with exchange.

See also

read_hdx calculate_exp_masses

Examples

plot_uncertainty(alpha_dat)
#> Warning: Removed 107 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

plot_uncertainty(alpha_dat, aggregated = FALSE)
#> Warning: Removed 45 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

plot_uncertainty(alpha_dat, aggregated = FALSE, separate_times = FALSE)
#> Warning: Removed 45 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

plot_uncertainty(alpha_dat, skip_amino = 1)
#> Warning: Removed 107 rows containing missing values or values outside the scale range
#> (`geom_segment()`).