PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration

In PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration

Introduction

This vignette demonstrates how to use PepMapViz with input files.

Accessing Input Files

The input files are stored in the inst/extdata/ directory of the package. You can access them using the system.file() function. The example files are searching results from PEAKS software. "Donor" column is added to plot peptides from different donors.

library(PepMapViz)

# Access the input files
input_file_folder <- system.file("extdata", package = "PepMapViz")

# Read the input files
resulting_df <- combine_files_from_folder(input_file_folder)
head(resulting_df)

Strip the sequence

This function takes outputs from multiple platform, a data frame with a column containing peptide sequences with modifications and converts it into a new dataframe with plain peptide sequences without modifications.

# Strip the sequence
striped_data_peaks <- strip_sequence(resulting_df, "Peptide", "Sequence", "PEAKS")
head(striped_data_peaks)

Extract modifications information

This function takes outputs from multiple platform, a data frame with a column containing modified peptide sequence with the detailed post translational modification(PTM) information and converts it into a new dataframe with plain peptide sequences and associated PTM information.

# Extract modifications information
PTM_table <- data.frame(PTM_mass = c("15.99", ".98", "57.02", "42.01"),
                        PTM_type = c("Ox", "Deamid", "Cam", "Acetyl"))
converted_data_peaks <- obtain_mod(
  striped_data_peaks,
  "Peptide",
  "PEAKS",
  strip_seq_col = NULL,
  PTM_table,
  PTM_annotation = TRUE,
  PTM_mass_column = "PTM_mass"
)
head(converted_data_peaks)

Match peptide sequence with provided sequence and calculate positions

This function matches peptide sequences from the 'peptide_data' data frame to corresponding provided whole sequences in the 'whole_seq' data frame. It calculates the start and end positions of the matched sequences and returns data frame with information about the matching positions.

# Match peptide sequence with provided sequence and calculate positions
whole_seq <- data.frame(
  Epitope = c("Boco", "Boco"),
  Chain = c("HC", "LC"),
  Region_Sequence = c("QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYYMHWVRQAPGQGLEWMGEISPFGGRTNYNEKFKSRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARERPLYASDLWGQGTTVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYTCNVDHKPSNTKVDKTVERKCCVECPPCPAPPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPSSIEKTISKTKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK", 
                      "DIQMTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYSASYRYTGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQRYSLWRTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC"
  )
)
matching_result <- match_and_calculate_positions(
  converted_data_peaks,
  'Sequence',
  whole_seq,
  match_columns = NULL,
  sequence_length = c(10, 30),
  column_keep = c(
    "PTM_mass",
    "PTM_position",
    "reps",
    "Area",
    "Donor",
    "PTM_type"
  )
)
head(matching_result)

Quantify matched peptide sequences

This function takes peptide matching result and quantifies the matched peptide sequences based on the provided quantification method. If the quantification method is 'PSM', the function calculates the number of matched peptide sequences in each positions of the provided whole sequence. If the quantification method is 'Area', the function select the max value in area column of identical peptide sequences and calculates the sum of the areas of the matched peptide sequences in each positions of the provided whole sequence.

# Quantify matched peptide sequences by PSM
matching_columns = c("Chain", "Epitope")
distinct_columns = c("Donor")
data_with_psm <- peptide_quantification(
  whole_seq,
  matching_result,
  matching_columns,
  distinct_columns,
  quantify_method = "PSM",
  with_PTM = TRUE,
  reps = TRUE
)
region <- data.frame(
  Epitope = c("Boco", "Boco", "Boco", "Boco", "Boco", "Boco"),
  Chain = c("HC", "HC", "HC", "HC", "LC", "LC"),
  Region = c("VH", "CH1", "CH2", "CH3", "VL", "CL"),
  Region_start = c(1,119,229,338,1,108),
  Region_end = c(118,228,337,444,107,214)
)
result_with_psm <- data.frame()
for (i in 1:nrow(region)) {
  chain <- region$Chain[i]
  region_start <- region$Region_start[i]
  region_end <- region$Region_end[i]
  region_name <- region$Region[i]

  temp <- data_with_psm[data_with_psm$Chain == chain & 
                          data_with_psm$Position >= region_start & 
                          data_with_psm$Position <= region_end, ]
  temp$Region <- region_name

  result_with_psm <- rbind(result_with_psm, temp)
}

head(result_with_psm)

Plotting peptide in whole provided sequence

This function takes the quantified peptide data frame and plots the matched peptide sequences in the provided whole sequence. The function returns a ggplot object with the matched peptide sequences plotted in the provided whole sequence.

# Plotting peptide in whole provided sequence
domain <- data.frame(
  domain_type = c("CDR H1", "CDR H2", "CDR H3", "CDR L1", "CDR L2", "CDR L3"),
  Region = c("VH", "VH", "VH",  "VL", "VL", "VL"),
  Epitope = c("Boco", "Boco", "Boco", "Boco", "Boco", "Boco"),
  domain_start = c(26, 50, 97,  24, 50, 89),
  domain_end = c(35, 66, 107,  34, 56, 97)
)
x_axis_vars <- c("Region")
y_axis_vars <- c("Donor")
column_order <- list(
    Donor = "D1,D2,D3,D4,D5,D6,D7,D8",
    Region = "VH,CH1,CH2,CH3,VL,CL"
)
domain_color <- c(
"CDR H1" = "#F8766D",
"CDR H2" = "#B79F00",
"CDR H3" = "#00BA38",
"CDR L1" = "#00BFC4",
"CDR L2" = "#619CFF",
"CDR L3" = "#F564E3"
)
PTM_color <- c(
  "Ox" = "red",
  "Deamid" = "cyan",
  "Cam" = "blue",
  "Acetyl" = "magenta"
)
label_value = list(Donor = "D1")
p_psm <- create_peptide_plot(
  result_with_psm,
  y_axis_vars,
  x_axis_vars,
  y_expand = c(0.2, 0.2),
  x_expand = c(0.5, 0.5),
  theme_options = list(legend.box = "horizontal"),
  labs_options = list(title = "PSM Plot", x = "Position", fill = "PSM"),
  color_fill_column = 'PSM',
  fill_gradient_options = list(limits = c(0, 160)),  # Set the limits for the color scale
  label_size = 1.9,
  add_domain = TRUE,
  domain = domain,
  domain_start_column = "domain_start",
  domain_end_column = "domain_end",
  domain_type_column = "domain_type",
  domain_color = domain_color,
  PTM = TRUE,
  PTM_type_column = "PTM_type",
  PTM_color = PTM_color,
  add_label = TRUE,
  label_column = "Character",
  label_value = label_value,
  column_order = column_order
)
print(p_psm)

PepMapViz documentation built on April 3, 2025, 6:29 p.m.