PlotListOfCatalogsToPdf: Plot List of catalogs to Pdf

In steverozen/mSigAct.server: Shiny Server for Analyzing Mutational Signature Activities

Plot List of catalogs to Pdf

Description

Plot List of catalogs to Pdf

Usage

PlotListOfCatalogsToPdf(
  list.of.catalogs,
  file,
  plot.SBS12 = FALSE,
  cex = 0.8,
  grid = TRUE,
  upper = TRUE,
  xlabels = TRUE,
  ylim = NULL
)

Arguments

list.of.catalogs	List of catalogs in ICAMS format.
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. Taken from par("cex") by default. Only implemented for SBS96Catalog, SBS192Catalog and DBS144Catalog.
grid	A logical value indicating whether to draw grid lines. Only implemented for SBS96Catalog, DBS78Catalog, IndelCatalog, ID166Catalog.
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, ID166Catalog.
xlabels	A logical value indicating whether to draw x axis labels. Only implemented for SBS96Catalog, DBS78Catalog, IndelCatalog, ID166Catalog. If FALSE then plot x axis tick marks for SBS96Catalog; set par(tck = 0) to suppress.
ylim	Has the usual meaning. Only implemented for SBS96Catalog, IndelCatalog, ID166Catalog.

steverozen/mSigAct.server documentation built on July 9, 2023, 4:52 a.m.