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
)
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.
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"
.
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.
Has the usual meaning. Taken from par("cex")
by default.
Only implemented for SBS96Catalog, SBS192Catalog and DBS144Catalog.
A logical value indicating whether to draw grid lines. Only implemented for SBS96Catalog, DBS78Catalog, IndelCatalog.
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.
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.
A logical value indicating whether to draw y axis labels. Only implemented for SBS96Catalog, DBS78Catalog, IndelCatalog.
Has the usual meaning. Only implemented for SBS96Catalog and IndelCatalog.
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 *, \(Q<0.05\); **,
\(Q<0.01\); ***, \(Q<0.001\).
file <- system.file("extdata",
"strelka.regress.cat.sbs.96.csv",
package = "ICAMS")
catSBS96 <- ReadCatalog(file)
colnames(catSBS96) <- "sample"
PlotCatalog(catSBS96)
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