fortify_matrix.matrix_oncoplot: Build a Matrix for OncoPrint

In ggalign: A 'ggplot2' Extension for Consistent Axis Alignment

Build a Matrix for OncoPrint

Description

Converts a matrix suitable for creating an OncoPrint. tune.matrix() helps convert matrix object to a matrix_oncoplot object.

Usage

## S3 method for class 'matrix_oncoplot'
fortify_matrix(
  data,
  ...,
  genes = NULL,
  n_top = NULL,
  remove_empty_genes = TRUE,
  remove_empty_samples = TRUE,
  missing_genes = "error",
  data_arg = NULL,
  call = NULL
)

Arguments

data	A matrix where each row represents an genes, and each column represents samples. The values in the matrix indicate whether the element is part of the set.
...	These dots are for future extensions and must be empty.
genes	An atomic character defines the genes to draw.
n_top	A single number indicates how many top genes to be drawn.
remove_empty_genes	A single boolean value indicats whether to drop genes without any genomic alterations.
remove_empty_samples	A single boolean value indicats whether to drop samples without any genomic alterations.
missing_genes	A string, either "error" or "remove", specifying the action for handling missing genes.
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

• gene_summary: An integer vector of the altered samples for each gene.

• sample_summary: An integer vector of the altered genes for each sample.

• n_genes: Total number of genes.

• n_samples: Total number of samples.

See Also

tune.matrix()

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

ggalign documentation built on June 8, 2025, 11:25 a.m.