Volcano plot

Volcano plot for differential deuterim uptake between two biological states

Usage

plot_volcano(
  p_dat,
  state_1 = "",
  state_2 = "",
  adjust_axes = TRUE,
  show_confidence_limits = FALSE,
  confidence_level = 0.98,
  color_times = TRUE,
  show_insignificant_grey = FALSE,
  hide_insignificant = FALSE,
  fractional = FALSE,
  theoretical = FALSE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

p_dat: data produced by the create_p_diff_uptake_dataset function
state_1: selected biological state for given protein
state_2: selected biological state for given protein
adjust_axes: logical, indicator if the X-axis is symmetrical in relation to 0
show_confidence_limits: logical, indicates if the hybrid test confidence levels are shown
confidence_level: confidence level for the test, from range [0, 1]. It should be the same as used to prepare p_dat
color_times: logical, indicator if different time points are distinguishable by color
show_insignificant_grey: logical, indicator if the values not passing the test are shown in grey
hide_insignificant: logical, indicator if the values not passing the test are hidden
fractional: logical, indicator if values are shown in fractional form
theoretical: logical, indicator if values are calculated using theoretical controls
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_volcano generates the volcano plot based on supplied p_dat. On X-axis there is differential deuterium uptake in selected form. On Y-axis there is the P-value from t-Student test between two biological states. Based on selected confidence level, the confidence limits are calculated to indicate statistically significant values - shown as red dotted lines. The values that are in upper left and right corners pass the hybrid 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).

Houde, D., Berkowitz, S.A., and Engen, J.R. (2011). The Utility of Hydrogen/Deuterium Exchange Mass Spectrometry in Biopharmaceutical Comparability Studies. J Pharm Sci 100, 2071–2086.

Examples

p_dat <- create_p_diff_uptake_dataset(alpha_dat)
plot_volcano(p_dat, show_confidence_limits = TRUE)
#> Warning: All aesthetics have length 1, but the data has 636 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 636 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 636 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 636 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: Removed 191 rows containing missing values or values outside the scale range
#> (`geom_point()`).


plot_volcano(p_dat, show_confidence_limits = TRUE, show_insignificant_grey = TRUE)
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: Removed 116 rows containing missing values or values outside the scale range
#> (`geom_point()`).

plot_volcano(p_dat, show_confidence_limits = TRUE, hide_insignificant = TRUE)
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.

plot_volcano(p_dat, show_confidence_limits = TRUE, hide_insignificant = TRUE, show_insignificant_grey = TRUE)
#> Chosen parameters are in conflict. The unsignifiant values are in grey.
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 94 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: Removed 116 rows containing missing values or values outside the scale range
#> (`geom_point()`).