robot_2states_indexes {HDXBoxeR} | R Documentation |
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
)
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. |
Value
Robot maps for timecourses for 2 protein states and selected indexes.
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)