plot_exposure_to_pdf {mSigTools}

Plot exposures in multiple plots to a single PDF file, with each plot showing exposures for a manageable number of samples.

Description

Plot exposures in multiple plots to a single PDF file, with each plot showing exposures for a manageable number of samples.

Usage

plot_exposure_to_pdf(
  exposure,
  file,
  mfrow = c(2, 1),
  mar = c(6, 4, 3, 2),
  oma = c(3, 2, 0, 2),
  samples.per.line = 30,
  plot.proportion = FALSE,
  xlim = NULL,
  ylim = NULL,
  legend.x = NULL,
  legend.y = NULL,
  cex.legend = 0.9,
  cex.yaxis = 1,
  cex.xaxis = NULL,
  plot.sample.names = TRUE,
  yaxis.labels = NULL,
  width = 8.2677,
  height = 11.6929,
  ...
)

Arguments

exposure

Exposures as a numerical matrix (or data.frame) with signatures in rows and samples in columns. Rownames are taken as the signature names and column names are taken as the sample IDs. If you want exposure sorted from largest to smallest, use sort_exposure. Do not use column names that start with multiple underscores. The exposures will often be mutation counts, but could also be e.g. mutations per megabase.

file

The name of the PDF file to be produced.

mfrow

A vector of the form c(nr, nc). Subsequent figures will be drawn in an nr-by-nc array on the device by rows.

mar

A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot.

oma

A vector of the form c(bottom, left, top, right) giving the size of the outer margins in lines of text.

samples.per.line

Number of samples to show in each plot.

plot.proportion

Plot exposure proportions rather than counts.

xlim, ylim

Limits for the x and y axis. If NULL(default), the function tries to do something reasonable.

legend.x, legend.y

The x and y co-ordinates to be used to position the legend.

cex.legend

A numerical value giving the amount by which legend plotting text and symbols should be magnified relative to the default.

cex.yaxis

A numerical value giving the amount by which y axis values should be magnified relative to the default.

cex.xaxis

A numerical value giving the amount by which x axis values should be magnified relative to the default. If NULL(default), the function tries to do something reasonable.

plot.sample.names

Whether to plot sample names below the x axis. Default is TRUE. Ignored if there are no column names on exposure.

yaxis.labels

User defined y axis labels to be plotted. If NULL(default), the function tries to do something reasonable.

width, height

The width and height of the graphics region in inches.

...

Other arguments passed to barplot. If ylab is not included, it defaults to a value depending on plot.proportion. If col is not supplied the function tries to do something reasonable.

Value

An invisible list. The first element is a logical value indicating whether the plot is successful. The second element is a numeric vector giving the coordinates of the bar x-axis midpoints drawn, useful for adding to the graph.

Examples

file <- system.file("extdata",
  "Liver-HCC.exposure.csv",
  package = "mSigTools"
)
exposure <- read_exposure(file)
plot_exposure_to_pdf(exposure,
  file = file.path(tempdir(), "Liver-HCC.exposure.pdf"),
  cex.yaxis = 0.8, plot.proportion = TRUE
)