PlotCatalog: Plot one spectrum or signature
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Description Usage Arguments Value Comments Note Examples

Plot the spectrum of one sample or plot one signature. 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.

PlotCatalog(
  catalog,
  plot.SBS12 = NULL,
  cex = NULL,
  grid = NULL,
  upper = NULL,
  xlabels = NULL,
  ylabels = NULL,
  ylim = NULL
)

`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"`.
`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.
`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.

An invisible list whose first element is a logic value indicating whether the plot is successful. For SBS96Catalog, SBS192Catalog, DBS78Catalog, DBS144Catalog and IndelCatalog, the list will have a second element, which is a numeric vector giving the coordinates of all the bar midpoints drawn, useful for adding to the graph. For SBS192Catalog with "counts" catalog.type and non-NULL abundance and plot.SBS12 = TRUE, the list will have an additional element which is a list containing the strand bias statistics.

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.

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+.

file <- system.file("extdata",
                    "strelka.regress.cat.sbs.96.csv",
                    package = "ICAMS")
catSBS96 <- ReadCatalog(file)
colnames(catSBS96) <- "sample"
PlotCatalog(catSBS96)