Skip to contents

Manhattan plot

plot_manhattan.Rd

Manhattan plot with p-values from the t-Student test and peptide position.

Usage

plot_manhattan(
  p_dat,
  skip_amino = 0,
  plot_title = NULL,
  separate_times = TRUE,
  times = NULL,
  confidence_level = NULL,
  show_confidence_limit = TRUE,
  show_peptide_position = FALSE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

p_dat

data produced by the create_p_diff_uptake_dataset function.

skip_amino

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

plot_title

title for the plot. If not provided, it is constructed in a form: "Differences between state_1 and state_2"

separate_times

logical, indicates if the data should be seen on the same plot, or on separate plots for each time point of measurement.

times

vector of time points of measurements to be included in the plot.

confidence_level

confidence level for the test, from range [0, 1].

show_confidence_limit

logical, indicates if the hybrid testing confidence intervals are shown.

show_peptide_position

logical, indicates if the peptide length and position in the sequence is shown. Otherwise, the peptides are represented by their ID.

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 manhattan plot presents the P-values from t-student test, to see the regions of the protein with statistically significant changes between two biological states. 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 P-value from t-Student test.

References

Hageman, T. S. & Weis, D. D. Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach. Anal Chem 91, 8008–8016 (2019).

See also

read_hdx create_p_diff_uptake_dataset

Examples

p_dat <- create_p_diff_uptake_dataset(alpha_dat)
plot_manhattan(p_dat)
#> Warning: Removed 191 rows containing missing values or values outside the scale range
#> (`geom_point()`).

plot_manhattan(p_dat, separate_times = FALSE)
#> Warning: Removed 191 rows containing missing values or values outside the scale range
#> (`geom_point()`).

plot_manhattan(p_dat, show_peptide_position = TRUE, separate_times = FALSE)
#> Warning: Removed 191 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

plot_manhattan(p_dat, separate_times = FALSE, show_confidence_limit = FALSE)
#> Warning: Removed 191 rows containing missing values or values outside the scale range
#> (`geom_point()`).