PepMapViz (version 1.1.0)

create_peptide_plot: Create a peptide Plot

Description

This function generates a peptide plot using the provided data and allows for customization of the plot layout.

Usage

create_peptide_plot(
  data,
  y_axis_vars,
  x_axis_vars,
  y_expand = c(0.1, 0.15),
  x_expand = c(0.6, 0.6),
  theme_options = NULL,
  labs_options = NULL,
  color_fill_column,
  fill_gradient_options = list(),
  label_size = 3,
  add_domain = TRUE,
  domain = NULL,
  domain_start_column = "domain_start",
  domain_end_column = "domain_end",
  domain_type_column = "domain_type",
  domain_border_color_column = NULL,
  domain_fill_color_column = NULL,
  add_domain_label = TRUE,
  domain_label_size = 4,
  domain_label_y_column = NULL,
  domain_label_color = "black",
  PTM = FALSE,
  PTM_type_column = "PTM_type",
  PTM_color = NULL,
  add_label = TRUE,
  label_column = "Character",
  label_filter = NULL,
  label_y = 1.28,
  column_order = NULL
)

Value

This function returns a ggplot object representing the PSM plot.

Arguments

data

A dataframe containing the PSM data or Area data got from peptide_cluster_quantification.

y_axis_vars

A list of variables for the donor and type facets.

x_axis_vars

A list of variables for the region facets.

y_expand

A numeric vector of length 2 specifying the expansion for the y-axis. Default is c(0.1, 0.15).

x_expand

A numeric vector of length 2 specifying the expansion for the x-axis. Default is c(0.6, 0.6).

theme_options

A list of additional theme options to customize the plot. Default is an empty list.

labs_options

A list of additional labs options to customize the plot labels. Default is an empty list.

color_fill_column

The name of the column in data_with_psm to be used for the fill aesthetic. Default is 'PSM'.

fill_gradient_options

A list of options for scale_fill_gradient. Default is an empty list.

label_size

The size of the labels in the plot. Default is 3.

add_domain

A logical value indicating whether to add domain like CDR (Complementarity-Determining Region) to the plot. Default is TRUE.

domain

A dataframe containing the domain data with columns including 'domain_start', 'domain_end', and 'domain_type'.

domain_start_column

The name of the column in domain containing the start position of the domain Default is 'domain_start'.

domain_end_column

The name of the column in domain containing the end position of the domain Default is 'domain_end'.

domain_type_column

The name of the column in domain containing the type of the domain Default is 'domain_type'.

domain_border_color_column

The name of the column in domain containing the border color of the domain Default is 'domain_color'.

domain_fill_color_column

The name of the column in domain containing the fill color of the domain Default is 'domain_fill_color'.

add_domain_label

Logical; whether to annotate the domain type as text above the domain rectangle. Default is TRUE.

domain_label_size

Numeric; text size for the domain label. Default is 4.

domain_label_y_column

The name of the column in domain containing y-axis position for the domain label. Default is 'domain_label_y'.

domain_label_color

Character; color for domain label text. Default is 'black'.

PTM

A logical value indicating whether to include PTM (Post-Translational Modification) data in the plot. Default is FALSE.

PTM_type_column

The name of the column in data_with_psm containing the type of the PTM. Default is 'PTM_type'.

PTM_color

A list of colors for the PTM types. Default is NULL.

add_label

A logical value indicating whether to add labels to the plot. Default is TRUE.

label_column

The name of the column in data_with_psm containing the labels to be added to the plot. Default is 'Character'.

label_filter

A list of column names and their values to filter the data for the labels. Default is NULL.

label_y

The position of y axis of the label.

column_order

A list of column names and their order for the plot. Default is NULL.

Examples

data <- data.frame(
  Character = c("X", "Y", "Z", "A", "A", "A"),
  Position = 1:6,
  Condition_1 = rep("Drug1", 6),
  Region_2 = rep("Arm_1", 6),
  Area = c(0.000000, 0.000000, 0.000000, 6.643856, 6.643856, 6.643856),
  Condition_2 = rep("Donor1", 6),
  Region_1 = rep("VH", 6),
  PTM = c(FALSE, TRUE, FALSE, FALSE, FALSE, FALSE),
  PTM_type = c(NA, "O", NA, NA, NA, NA)
)
domain <- data.frame(
  domain_type = c("CDR H1", "CDR H2", "CDR H3"),
  Region_1 = c("VH", "VH", "VH"),
  Region_2 = c("Arm_1", "Arm_1", "Arm_1"),
  Condition_1 = c("Drug1", "Drug1", "Drug1"),
  domain_start = c(1, 3, 5),
  domain_end = c(2, 4, 6),
  domain_color = c("#F8766D", "#B79F00", "#00BA38"),
  domain_fill_color = c("#F8766D", "#B79F00", "#00BA38"),
  domain_label_y = c(1.35, 1.35, 1.35)
)
x_axis_vars <- c("Region_2", "Region_1")
y_axis_vars <- c("Condition_2")
PTM_color <- c(
  "Ox" = "red",
  "Deamid" = "cyan",
  "Cam" = "blue",
  "Acetyl" = "magenta"
)
p <- create_peptide_plot(
  data,
  y_axis_vars,
  x_axis_vars,
  y_expand = c(0.2, 0.2),
  x_expand = c(0.5, 0.5),
  theme_options = list(),
  labs_options = list(title = "Area Plot", x = "Position", fill = "Area"),
  color_fill_column = 'Area',
  fill_gradient_options = list(),
  label_size = 5,
  add_domain = TRUE,
  domain = domain,
  domain_start_column = "domain_start",
  domain_end_column = "domain_end",
  domain_type_column = "domain_type",
  domain_border_color_column = "domain_color",
  domain_fill_color_column = "domain_fill_color",
  add_domain_label = TRUE,
  domain_label_size = 4,
  domain_label_y_column = "domain_label_y",
  domain_label_color = "black",
  PTM = FALSE,
  PTM_type_column = "PTM_type",
  PTM_color = PTM_color,
  add_label = TRUE,
  label_column = "Character",
  label_filter = NULL,
  label_y = 1,
  column_order = list(Region_1 = 'VH')
)
print(p)