Build a matrix from a maftools object
Usage
# S3 method for class 'GISTIC'
fortify_matrix(
data,
...,
n_top = NULL,
bands = NULL,
ignored_bands = NULL,
sample_anno = NULL,
remove_empty_samples = TRUE,
data_arg = NULL,
call = NULL
)
Arguments
- data
A
GISTIC
object.- ...
These dots are for future extensions and must be empty.
- n_top
A single number indicates how many top bands to be drawn.
- bands
An atomic character defines the bands to draw.
- ignored_bands
An atomic character defines the bands to be ignored.
- sample_anno
A data frame of sample clinical features to be added.
- remove_empty_samples
A single boolean value indicating whether to drop samples without any genomic alterations.
- data_arg
The argument name for
data
. Developers can use it to improve messages. Not used by the user.- call
The execution environment where
data
and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.
ggalign attributes
sample_anno
: sample clinical informations provided insample_anno
.sample_summary
: sample copy number summary informations. Seedata@cnv.summary
for details.cytoband_summary
: cytoband summary informations. Seedata@cytoband.summary
for details.gene_summary
: gene summary informations. Seedata@gene.summary
for details.summary
: A data frame of summary information. Seedata@summary
for details.