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
dataand 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.