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)