PlotCatalogToPdf: Plot catalog to a PDF file

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Plot catalog to a PDF file

Description

Plot catalog to a PDF file. The type of graph is based on 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,
  ylabels = NULL,
  ylim = NULL
)

Arguments

catalog	A catalog as defined in ICAMS with attributes added. See as.catalog for more details. catalog can also be a numeric matrix, numeric data.frame, or a vector denoting the mutation counts, but must be in the correct row order used in ICAMS. See CatalogRowOrder for more details. If catalog is a vector, it will be converted to a 1-column matrix with rownames taken from the element names of the vector and with column name "Unknown".
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	Has the usual meaning. A default value has been used by the program internally. Only implemented for SBS96Catalog, SBS192Catalog and DBS144Catalog.
grid	A logical value indicating whether to draw grid lines. Only implemented for SBS96Catalog, DBS78Catalog, IndelCatalog.
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, DBS78Catalog, IndelCatalog.
xlabels	A logical value indicating whether to draw x axis labels. Only implemented for SBS96Catalog, DBS78Catalog, IndelCatalog. If FALSE then plot x axis tick marks for SBS96Catalog; set par(tck = 0) to suppress.
ylabels	A logical value indicating whether to draw y axis labels. Only implemented for SBS96Catalog, DBS78Catalog, IndelCatalog.
ylim	Has the usual meaning. Only implemented for SBS96Catalog and IndelCatalog.

Value

An invisible list whose first element is a logic value indicating whether the plot is successful. For SBS192Catalog with "counts" catalog.type and non-null abundance and plot.SBS12 = TRUE, the list will have a second element which is a list containing the strand bias statistics.

Comments

For SBS192Catalog with "counts" catalog.type and non-NULL abundance and plot.SBS12 = TRUE, the strand bias statistics are Benjamini-Hochberg q-values based on two-sided binomial tests of the mutation counts on the transcribed and untranscribed strands relative to the actual abundances of C and T on the transcribed strand. On the SBS12 plot, asterisks indicate q-values as follows *, Q<0.05; **, Q<0.01; ***, Q<0.001.

Note

The sizes of repeats involved in deletions range from 0 to 5+ in the mutational-spectra and signature catalog rownames, but for plotting and end-user documentation deletion repeat sizes range from 1 to 6+.

Examples

file <- system.file("extdata",
                    "strelka.regress.cat.sbs.96.csv",
                    package = "ICAMS")
catSBS96 <- ReadCatalog(file)
colnames(catSBS96) <- "sample"
PlotCatalogToPdf(catSBS96, file = file.path(tempdir(), "test.pdf"))

ICAMS documentation built on June 22, 2024, 6:47 p.m.