woods_plot: Plot Woods' plot

In HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Description

Produces Woods' plot based on theoretical or experimental HDX-MS data.

Usage

woods_plot(
  calc_dat,
  theoretical = FALSE,
  relative = TRUE,
  confidence_limit = 0.98,
  confidence_limit_2 = 0.99
)

Arguments

calc_dat	data as imported by the read_hdx function and processed by the prepare_dataset function.
theoretical	logical, determines if plot shows theoretical values.
relative	logical, determines if values are relative or absolute.
confidence_limit	confidence limit.
confidence_limit_2	confidence limit 2.

Details

...

This is the first version - multi-state calculations are not supported.

Value

a ggplot object.

References

Woods, V.L., and Hamuro, Y. (2001). High resolution, high-throughput amide deuterium exchange-mass spectrometry (DXMS) determination of protein binding site structure and dynamics: utility in pharmaceutical design. J. Cell. Biochem. Suppl. Suppl 37, 89–98.

See Also

read_hdx prepare_dataset

Examples

# load example data
dat <- read_hdx(system.file(package = "HaDeX", 
                            "HaDeX/data/KD_180110_CD160_HVEM.csv"))
                            
# prepare dataset for states `CD160` and `CD160_HVEM` 
# in given time parameters                           
calc_dat <- prepare_dataset(dat,
                            in_state_first = "CD160_0.001",
                            chosen_state_first = "CD160_1",
                            out_state_first = "CD160_1440",
                            in_state_second = "CD160_HVEM_0.001",
                            chosen_state_second = "CD160_HVEM_1",
                            out_state_second = "CD160_HVEM_1440") 
                            
# plot Woods plot - theoretical & relative                             
woods_plot(calc_dat = calc_dat,
           theoretical = TRUE,
           relative = TRUE,
           confidence_limit = 0.98,
           confidence_limit_2 = 0.99)
           
# plot Woods plot - experimental  & relative                
woods_plot(calc_dat = calc_dat,
           theoretical = FALSE,
           relative = TRUE,
           confidence_limit = 0.98,
           confidence_limit_2 = 0.99)

# plot Woods plot - theoretical & absolute    
woods_plot(calc_dat = calc_dat,
           theoretical = TRUE,
           relative = FALSE,
           confidence_limit = 0.98,
           confidence_limit_2 = 0.99)

# plot Woods plot - experimental & absolute    
woods_plot(calc_dat = calc_dat,
           theoretical = FALSE,
           relative = FALSE,
           confidence_limit = 0.98,
           confidence_limit_2 = 0.99)
            

HaDeX documentation built on Aug. 12, 2021, 5:20 p.m.