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plot_DBS136, plot_DBS136_pdf, plot_SBS1536, plot_SBS1536_pdf

Source: R/plot_DBS136.R, R/plot_DBS136_pdf.R, R/plot_SBS1536.R, and 1 more
heatmap_plots.Rd

Plot functions for SBS and DBS mutational signature catalogs as heatmaps. All functions return ggplot2 objects.

Usage

plot_DBS136(
  catalog,
  plot_title = NULL,
  base_size = 11,
  plot_title_cex = 1.2,
  axis_text_cex = 0.8,
  strip_text_cex = 1,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE
)

plot_DBS136_pdf(catalog, filename, ...)

plot_SBS1536(
  catalog,
  plot_title = NULL,
  base_size = 11,
  plot_title_cex = 1.2,
  axis_text_cex = 0.8,
  strip_text_cex = 1,
  show_axis_text_x = TRUE,
  show_axis_text_y = TRUE,
  show_axis_title_x = TRUE,
  show_axis_title_y = TRUE
)

plot_SBS1536_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.

base_size

Numeric. Base font size in points.

plot_title_cex

Numeric. Multiplier for the plot title size.

axis_text_cex

Numeric. Multiplier for axis label size.

strip_text_cex

Numeric. Multiplier for panel/facet label size.

show_axis_text_x

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

show_axis_text_y

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

show_axis_title_x

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

show_axis_title_y

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

filename

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

...

Additional arguments passed to the underlying plot function (\_pdf variants 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_SBS1536: SBS pentanucleotide context (1536 channels)

  • plot_DBS136: DBS heatmap (136 channels, 10 4x4 panels)

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

Examples

set.seed(1)
sig <- runif(136)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$DBS136
plot_DBS136(sig, plot_title = "Example DBS136")


set.seed(1)
sig <- runif(1536)
sig <- sig / sum(sig)
names(sig) <- catalog_row_order()$SBS1536
plot_SBS1536(sig, plot_title = "Example SBS1536")