ICAMS (version 2.0.7)

PlotCatalogToPdf: Plot catalog to a PDF file.

Description

Plot catalog to a PDF file. The type of graph is based on one attribute("catalog.type") of the input catalog. You can first use TransformCatalog to get different types of catalog and then do the plotting.

Usage

PlotCatalogToPdf(catalog, file, plot.SBS12 = NULL, cex = NULL,
  grid = NULL, upper = NULL, xlabels = NULL)

Arguments

catalog

A catalog as defined in ICAMS with attributes added. See as.catalog for more details.

file

The name of the PDF file to be produced.

plot.SBS12

Only meaningful for class SBS192Catalog; if TRUE, generate an abbreviated plot of only SBS without context, i.e. C>A, C>G, C>T, T>A, T>C, T>G each on transcribed and untranscribed strands, rather than SBS in trinucleotide context, e.g. ACA > AAA, ACA > AGA, ..., TCT > TAT, ... There are 12 bars in the graph.

cex

A numerical value giving the amount by which mutation class labels, mutation counts(if it exists), y axis and its labels, x axis labels and its annotations(if it exists), sample name and legend(if it exists) should be magnified relative to the default. Only implemented for SBS96Catalog, SBS192Catalog and DBS144Catalog.

grid

A logical value indicating whether to draw grid lines. Only implemented for SBS96Catalog.

upper

A logical value indicating whether to draw horizontal lines and the names of major mutation class on top of graph. Only implemented for SBS96Catalog.

xlabels

A logical value indicating whether to draw x axis labels. Only implemented for SBS96Catalog.

Value

invisible(TRUE)

Examples

# NOT RUN {
file <- system.file("extdata",
                    "strelka.regress.cat.sbs.96.csv",
                    package = "ICAMS")
catSBS96 <- ReadCatalog(file, ref.genome = "hg19", 
                        region = "genome",
                        catalog.type = "counts")
colnames(catSBS96) <- "sample"
PlotCatalogToPdf(catSBS96, file = file.path(tempdir(), "test.pdf"))
# }