robot_plot_All: Returns a robot plot for comparisons of the timepoints...

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

Returns a robot plot for comparisons of the timepoints samples

Description

Modification of butterfly plot. x axis residues. y axis % deuteration for one variant above the axis and for second peptide below the axis. 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

robot_plot_All(
  thP,
  th,
  replicates = 3,
  pv_cutoff = 0.01,
  states,
  CI_factor = 1
)

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.

Value

Robot maps for timecourses

Examples

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
tm_df<-output_tc(filepath=file_nm)
tmP_df<-output_tc(filepath=file_nm, percent=TRUE)
robot_plot_All(thP = tmP_df, th=tm_df, pv_cutoff=0.001)

# more restrictive peptide selection
robot_plot_All(thP = tmP_df, th=tm_df, pv_cutoff=0.001, CI_factor=3)

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