Skip to contents

plot_DBS144, plot_DBS144_pdf, plot_DBS78, plot_DBS78_pdf, plot_ID166, plot_ID166_pdf, plot_ID476, plot_ID476_pdf, plot_ID476_right, plot_ID476_right_pdf, plot_ID83, plot_ID83_pdf, plot_ID89, plot_ID89_pdf, plot_SBS12, plot_SBS12_pdf, plot_SBS192, plot_SBS192_pdf, plot_SBS288, plot_SBS96, plot_SBS96_pdf

Source: R/plot_DBS144.R, R/plot_DBS144_pdf.R, R/plot_DBS78.R, and 18 more
bar_plots.Rd

Plot functions for SBS, DBS, and indel mutational signature catalogs as bar charts. All functions return ggplot2 objects.

Usage

plot_DBS144(
  catalog,
  plot_title = NULL,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE,
  ylim = NULL,
  base_size = 11,
  plot_title_cex = 0.8,
  axis_text_x_cex = 1,
  axis_title_x_cex = 1,
  axis_title_y_cex = 1,
  axis_text_y_cex = 0.8
)

plot_DBS144_pdf(catalog, filename, ...)

plot_DBS78(
  catalog,
  plot_title = NULL,
  grid = TRUE,
  upper = TRUE,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE,
  ylim = NULL,
  base_size = 11,
  plot_title_cex = 0.8,
  count_label_cex = 0.9,
  class_label_cex = 0.7,
  axis_text_x_cex = 0.5,
  axis_title_x_cex = 1,
  axis_title_y_cex = 1,
  axis_text_y_cex = 0.8,
  show_counts = NULL,
  num_peak_labels = 0,
  peak_label_cex = 0.7
)

plot_DBS78_pdf(catalog, filename, ...)

plot_ID166(
  catalog,
  plot_title = NULL,
  grid = TRUE,
  upper = TRUE,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE,
  ylim = NULL,
  base_size = 11,
  plot_title_cex = 0.8,
  count_label_cex = 0.9,
  block_label_cex = 0.65,
  class_label_cex = 0.8,
  axis_text_x_cex = 0.5,
  bottom_label_cex = 0.65,
  axis_title_x_cex = 1,
  axis_title_y_cex = 1,
  axis_text_y_cex = 0.8,
  show_counts = NULL,
  num_peak_labels = 0,
  peak_label_cex = 0.7
)

plot_ID166_pdf(catalog, filename, ...)

plot_ID476(
  catalog,
  plot_title = NULL,
  base_size = 11,
  plot_title_cex = 1,
  count_label_cex = 0.52,
  class_label_cex = 0.78,
  axis_text_x_cex = 0.8,
  axis_title_x_cex = 0.7,
  axis_title_y_cex = 0.9,
  axis_text_y_cex = 0.7,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE,
  show_counts = NULL,
  num_peak_labels = 4,
  peak_label_cex = 0.52,
  label_threshold_denominator = 7,
  vline_labels = c(),
  simplify_labels = FALSE,
  plot_complex = FALSE,
  stop_at_9 = TRUE
)

plot_ID476_pdf(catalog, filename, ...)

plot_ID476_right(
  catalog,
  plot_title = NULL,
  base_size = 11,
  plot_title_cex = 1,
  count_label_cex = 1.03,
  class_label_cex = 1,
  axis_text_x_cex = 0.7,
  axis_title_x_cex = 0.9,
  axis_title_y_cex = 0.9,
  axis_text_y_cex = 0.7,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE,
  show_counts = NULL,
  num_peak_labels = 3,
  peak_label_cex = 0.7,
  label_threshold_denominator = 7,
  vline_labels = c(),
  simplify_labels = TRUE,
  plot_complex = FALSE,
  stop_at_9 = TRUE
)

plot_ID476_right_pdf(catalog, filename, ...)

plot_ID83(
  catalog,
  plot_title = NULL,
  grid = TRUE,
  upper = TRUE,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE,
  ylim = NULL,
  base_size = 11,
  plot_title_cex = 0.8,
  count_label_cex = 0.9,
  block_label_cex = 0.65,
  class_label_cex = 0.8,
  axis_text_x_cex = 0.5,
  bottom_label_cex = 0.65,
  axis_title_x_cex = 1,
  axis_title_y_cex = 1,
  axis_text_y_cex = 0.8,
  show_counts = NULL,
  num_peak_labels = 0,
  peak_label_cex = 0.7
)

plot_ID83_pdf(catalog, filename, ...)

plot_ID89(
  catalog,
  plot_title = NULL,
  upper = TRUE,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE,
  ylim = NULL,
  base_size = 11,
  plot_title_cex = 1,
  count_label_cex = 1.03,
  block_label_cex = 3,
  class_label_cex = block_label_cex,
  axis_text_x_cex = 0.7,
  axis_title_x_cex = 0.9,
  axis_title_y_cex = 0.9,
  axis_text_y_cex = 0.7,
  show_counts = NULL,
  ylab = TRUE,
  show_extra_top_bar = FALSE,
  plot_complex = FALSE,
  num_peak_labels = 0,
  peak_label_cex = 0.7,
  stop_at_9 = TRUE
)

plot_ID89_pdf(catalog, filename, ...)

plot_SBS12(
  catalog,
  plot_title = NULL,
  abundance = NULL,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE,
  ylim = NULL,
  base_size = 11,
  plot_title_cex = 0.8,
  axis_text_x_cex = 1,
  axis_title_x_cex = 1,
  axis_title_y_cex = 1,
  axis_text_y_cex = 0.8
)

plot_SBS12_pdf(catalog, filename, ...)

plot_SBS192(
  catalog,
  plot_title = NULL,
  grid = TRUE,
  upper = TRUE,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE,
  ylim = NULL,
  base_size = 11,
  plot_title_cex = 0.8,
  count_label_cex = 0.9,
  class_label_cex = 0.9,
  axis_text_x_cex = 0.5,
  axis_title_x_cex = 1,
  axis_title_y_cex = 1,
  axis_text_y_cex = 0.8,
  show_counts = NULL,
  num_peak_labels = 0,
  peak_label_cex = 0.7
)

plot_SBS192_pdf(catalog, filename, ...)

plot_SBS288(catalog, plot_title = NULL, ...)

plot_SBS96(
  catalog,
  plot_title = NULL,
  grid = TRUE,
  upper = TRUE,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE,
  ylim = NULL,
  base_size = 11,
  plot_title_cex = 0.8,
  count_label_cex = 0.9,
  class_label_cex = 1.1,
  axis_text_x_cex = 0.7,
  axis_title_x_cex = 1,
  axis_title_y_cex = 1,
  axis_text_y_cex = 0.8,
  show_counts = NULL,
  num_peak_labels = 0,
  peak_label_cex = 0.7
)

plot_SBS96_pdf(catalog, filename, ...)

Arguments

catalog

Numeric vector, single-column data.frame, matrix, tibble, or data.table. If there are row names (or for a vector, names), they will be checked against catalog_row_order().

plot_title

Character. Title displayed above the plot.

show_axis_text_x

Logical. If FALSE, hide x-axis tick labels.

show_axis_text_y

Logical. If FALSE, hide y-axis tick labels.

show_axis_title_x

Logical. If FALSE, hide the x-axis title.

show_axis_title_y

Logical. If FALSE, hide the y-axis title.

ylim

Optional y-axis limits.

base_size

Numeric. Base font size in points.

plot_title_cex

Numeric. Multiplier for the plot title size.

axis_text_x_cex

Numeric. Multiplier for x-axis labels.

axis_title_x_cex

Numeric. Multiplier for x-axis title size. Currently has no effect in some functions.

axis_title_y_cex

Numeric. Multiplier for the y-axis title size.

axis_text_y_cex

Numeric. Multiplier for the y-axis tick label size.

filename

Character. Path to the output PDF file (\_pdf functions only).

...

Additional arguments passed to plot_SBS96() (plot_SBS288 only).

grid

Logical, draw grid lines.

upper

Logical, draw colored class rectangles and labels above bars.

count_label_cex

Numeric. Multiplier for per-class count labels.

class_label_cex

Numeric. Multiplier for major class labels.

show_counts

Logical or NULL. If TRUE, always display per-class count labels. If FALSE, never display them. If NULL (the default), display them only when the catalog contains counts (sum > 1.1).

num_peak_labels

Integer. Number of top peaks to label (0 = none).

peak_label_cex

Numeric. Size multiplier for peak labels.

block_label_cex

Numeric. Multiplier for colored category block labels (indel plots only).

bottom_label_cex

Numeric. Multiplier for bottom category description labels (indel plots only).

label_threshold_denominator

Numeric. Peaks below max/label_threshold_denominator are not labeled (plot_ID476, plot_ID476_right only).

vline_labels

Character vector. IndelType labels at which to draw vertical reference lines (plot_ID476, plot_ID476_right only).

simplify_labels

Logical. Simplify peak labels by removing the indel type prefix (plot_ID476, plot_ID476_right only).

plot_complex

Logical. Include Complex indel channels (plot_ID89, plot_ID476, plot_ID476_right only).

stop_at_9

Logical. If TRUE, cap repeat length labels at 9 (plot_ID89, plot_ID476, plot_ID476_right only).

ylab

Y-axis label control (plot_ID89 only). TRUE (default) auto-detects from data. A character string overrides the label. NULL or FALSE suppresses the y-axis title.

show_extra_top_bar

Logical. Display an extra summary bar above the category bar (plot_ID89 only).

abundance

Numeric vector of per-class abundances for strand bias testing (plot_SBS12 only).

Value

Plot functions return a ggplot2 object, or NULL with a warning if the catalog is invalid (wrong size or row names). PDF functions return NULL invisibly (called for side effect of creating a PDF file), or stop with an error if the catalog is invalid.

Details

Functions in this family:

  • plot_SBS96, plot_SBS192: SBS trinucleotide context

  • plot_DBS78: DBS dinucleotide substitutions

  • plot_DBS144: DBS with transcription strand

  • plot_SBS12: SBS strand bias summary (collapses 192 to 12 bars)

  • plot_SBS288: SBS with three-strand context

  • plot_ID166: Indel genic/intergenic (166 channels)

  • plot_ID83: Indel COSMIC classification (83 channels)

  • plot_ID89: Indel Koh classification (89 channels)

  • plot_ID476, plot_ID476_right: Indel with flanking context (476 channels)

Each has a corresponding _pdf() variant for multi-sample PDF export.

Examples

set.seed(1)
sig <- runif(144)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$DBS144
plot_DBS144(sig, plot_title = "Example DBS144 signature")


set.seed(1)
sig <- runif(78)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$DBS78
plot_DBS78(sig, plot_title = "Example DBS78 signature")


set.seed(1)
sig <- runif(166)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$ID166
plot_ID166(sig, plot_title = "Example ID166 signature")


set.seed(1)
sig <- runif(476)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$ID476
plot_ID476(sig, plot_title = "Example ID476")


set.seed(1)
sig <- runif(476)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$ID476
plot_ID476_right(sig, plot_title = "Example ID476 right panel")


set.seed(1)
sig <- runif(83)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$ID
plot_ID83(sig, plot_title = "Example ID83")


set.seed(1)
sig <- runif(89)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$ID89
plot_ID89(sig, plot_title = "Example ID89")


set.seed(1)
sig <- runif(192)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$SBS192
plot_SBS12(sig, plot_title = "Example SBS12 strand bias")


set.seed(1)
sig <- runif(192)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$SBS192
plot_SBS192(sig, plot_title = "Example SBS192 signature")


if (FALSE) { # \dontrun{
set.seed(1)
sig <- runif(288)
names(sig) <- catalog_row_order()$SBS288
plot_SBS288(sig, plot_title = "Example SBS288")
} # }

# Plot a random SBS96 signature (proportions summing to 1)
set.seed(1)
sig <- runif(96)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$SBS96
plot_SBS96(sig, plot_title = "Example SBS96 signature")