signature_plot: CpG signature plot

Description

CpG signature plot

Usage

signature_plot(
  cpg_obj,
  data,
  meta_data,
  sample_id_column,
  true_label_column,
  color_dict = NULL,
  color_others = "black",
  as_panel = TRUE,
  is_beta = TRUE,
  base_size = 14,
  ...
)

Value

A list with the data and the ggplot2 plot object.

Arguments

cpg_obj: A CimpleG object, as generated by the CimpleG function. Alternatively a names character vector or list with the signatures.
data: Matrix or data.frame that should have the samples and signatures to plot. Samples should be in rows and probes/CpGs in columns.
meta_data: Data.frame containing metadata from samples in `data`.
sample_id_column: Name of the column containing the sample id in the meta_data data.frame
true_label_column: Name of the column containing the true labels of the samples in the meta_data data.frame
color_dict: Named string featuring colors as values and labels (true labels) as names
color_others: The name or hex code of a color by which the non-target samples should be colored by.
as_panel: A boolean, if TRUE (default) a single figure panel with all the signatures will be generated. Otherwise, the individual plots will be returned as a list.
is_beta: A boolean, if TRUE (default) the values will be plotted in a scale suitable for Beta values. Otherwise, the values will be plotted in scale suitable for M values.
base_size: An integer defining the base size of the text in the plot. Default is `14`.
...: Parameters passed to the ggplot2::theme function.