HDXBoxeR (version 0.0.2)

plot_peptide_sig_tp_proc: Draws peptides with significant difefrences between sets.

Description

Returns plot where significant peptides are colored in blue-red scheme.

Usage

plot_peptide_sig_tp_proc(
  input_proc,
  input_up,
  nb_pep_row = 100,
  ranges = c(-Inf, seq(-30, 30, by = 10), Inf),
  pv_cutoff = 0.01,
  replicates = 3
)

Value

plot with peptides which are significantly different between sets.

Arguments

input_proc

Dataframe with organized procent deuteration data. Input generated using output_tp_proc() function.

input_up

Dataframe with organized deuteration uptake. Input generated using output_tp() function.

nb_pep_row

number of peptides in each row. Plotting parameter. Default set to 100.

ranges

ranges for coloring scheme. Default set to c(-Inf, seq(-30, 30, by=10), Inf)

pv_cutoff

p-value cutoff here set up to 0.01

replicates

number of replicates in sample. Default set to 3.

Examples

file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
a_up<- output_tp(file_nm)
a_proc<- output_tp(file_nm, percent=TRUE)
plot_peptide_sig_tp_proc(input_proc=a_proc, input_up=a_up, replicates=3, pv_cutoff=0.01,
ranges=c(-Inf,-40, -30,-20,-10, 0,10, 20,30,40, Inf), nb_pep_row=40 )