HDXBoxeR (version 0.0.2)

robot_2states_indexes: Returns a robot plot for selected peptides for 2 protein states.

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_2states_indexes(
  thP,
  th,
  indexes,
  states,
  replicates = 3,
  pvalue = 0.01,
  ylim,
  xlim,
  CI_factor = 1
)

Value

Robot maps for timecourses for 2 protein states and selected indexes.

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

indexes

indexes of peptides to be drawn.

states

Need to choose only two protein states

replicates

number of replicates in sample. Default set to 3.

pvalue

p-value cutoff here set up to 0.01

ylim

y-axis range

xlim

x-axis range. Set as default from max and minimum residues for the protein

CI_factor

Multiplication factor for Critical Interval. Allows for more restrictive selection of Critial interval.

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)
names_states<- nm_states(file_nm) ### returns states names
ind1<-robot_indexes(thP = tmP_df, th=tm_df, pvalue=0.001, CI_factor=3, states=names_states[1:2])
robot_2states_indexes(thP = tmP_df, th=tm_df,
 states=names_states[1:2],indexes =ind1, pvalue=0.001, CI_factor=3)