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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

logical, whether plot should have an interactive layer created with with ggiraph, which would add tooltips to the plot in an interactive display (HTML/Markdown documents or shiny app)

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()`).