Description Usage Arguments Value Comments Note Examples
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.
1 2 3 4 5 6 7 8 9 10 11 |
catalog |
A catalog as defined in |
file |
The name of the PDF file to be produced. |
plot.SBS12 |
Only meaningful for class |
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 |
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 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.
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+.
1 2 3 4 5 6 | 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"))
|
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