ggalign (version 1.0.1)

fortify_matrix.GISTIC: Build a matrix from a maftools object

Description

Build a matrix from a maftools object

Usage

# S3 method for 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 in sample_anno.

• sample_summary: sample copy number summary informations. See [e-mail] for details.

• cytoband_summary: cytoband summary informations. See [e-mail] for details.

• gene_summary: gene summary informations. See [e-mail] for details.

• summary: A data frame of summary information. See data@summary for details.

See Also

Other fortify_matrix() methods: fortify_matrix.MAF(), fortify_matrix.default(), fortify_matrix.list_upset(), fortify_matrix.matrix(), fortify_matrix.matrix_oncoplot(), fortify_matrix.matrix_upset(), fortify_matrix.phylo()