Converts a matrix suitable for creating an OncoPrint. tune.matrix()
helps convert matrix object to a matrix_oncoplot object.
# S3 method for 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
)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.
An atomic character defines the genes to draw.
A single number indicates how many top genes to be drawn.
A single boolean value indicats whether to drop genes without any genomic alterations.
A single boolean value indicats whether to drop samples without any genomic alterations.
A string, either "error" or "remove", specifying the
action for handling missing genes.
The argument name for data. Developers can use it to
improve messages. Not used by the user.
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.
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.
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()