woods_CI_plot: Returns a woods plot for comparisons of the timepoints...

In mkajano/HDXBoxeR: Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

Returns a woods plot for comparisons of the timepoints samples

Description

Modification of butterfly plot. x axis residues. y axis % deuteration for Peptides are compared between the sets for the significance change between sets. If there is significant change beteween sets peptides are plotted for all timepoints. Significanty different timepoints for the peptides are colored. Peptides ranges are plotted as a line at corresponding % deuteration values.

Usage

woods_CI_plot(
  thP,
  th,
  replicates = 3,
  pv_cutoff = 0.01,
  states,
  CI_factor = 1,
  ylim = c(0, 120),
  ...
)

Arguments

thP	output of output_tcourse_proc() function. Raw data for procent deuteration for time courses
th	output of output_tcourse() function. Raw data for uptake deuteration for time courses
replicates	number of replicates in sample. Default set to 3.
pv_cutoff	p-value cutoff here set up to 0.01
states	Protein states from the set. As default all states are chosen.
CI_factor	Multiplication factor for Critical Interval. Allows for more restrictive selection of Critial interval.
ylim	y axis limit
...	other variables

Value

Woods plots with chosen statistically different peptides

Examples

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
a<- output_tc(file_nm)
b<-output_tc(file_nm, percent=TRUE)
woods_CI_plot(thP=b, th=a, pv_cutoff = 0.001, CI_factor = 1, replicates=3)

mkajano/HDXBoxeR documentation built on April 23, 2024, 12:28 a.m.