deconvolution_barplot

Stacked barplot of deconvolution results

DNA methylation signatures are usually based on multivariate
approaches that require hundreds of sites for predictions. 'CimpleG'
is a method for the detection of small CpG methylation signatures used
for cell-type classification and deconvolution. 'CimpleG' is time
efficient and performs as well as top performing methods for cell-type
classification of blood cells and other somatic cells, while basing
its prediction on a single DNA methylation site per cell type (but
users can also select more sites if they so wish). Users can train
cell type classifiers ('CimpleG' based, and others) and directly apply
these in a deconvolution of cell mixes context. Altogether, 'CimpleG'
provides a complete computational framework for the delineation of
DNAm signatures and cellular deconvolution. For more details see Maié
et al. (2023) <doi:10.1186/s13059-023-03000-0>.

Tiago F.V. Maié

CimpleG

A Method to Identify Single CpG Sites for Classification and
Deconvolution

deconvolution_barplot function

<dl><dt>deconvoluted_data</dt>
<dd>Result from running `run_deconvolution`</dd>
<dt>meta_data</dt>
<dd>Data.frame containing metadata from deconvoluted samples</dd>
<dt>sample_id_column</dt>
<dd>Name of the column containing the sample id in the meta_data data.frame</dd>
<dt>true_label_column</dt>
<dd>Name of the column containing the true labels of the samples in the meta_data data.frame</dd>
<dt>color_dict</dt>
<dd>Named string featuring colors as values and labels (true labels) as names</dd>
<dt>show_x_label</dt>
<dd>A boolean, if `TRUE` the sample labels in the X axis will be shown. Default is `FALSE`.</dd>
<dt>base_size</dt>
<dd>An integer defining the base size of the text in the plot. Default is `14`.</dd>
<dt>...</dt>
<dd>Parameters passed to the ggplot2::theme function.</dd></dl>

Arguments

Stacked barplot of deconvolution results — deconvolution_barplot

<dl>

<dt>deconvoluted_data</dt>
<dd>Result from running `run_deconvolution`</dd>


<dt>meta_data</dt>
<dd>Data.frame containing metadata from deconvoluted samples</dd>


<dt>sample_id_column</dt>
<dd>Name of the column containing the sample id in the meta_data data.frame</dd>


<dt>true_label_column</dt>
<dd>Name of the column containing the true labels of the samples in the meta_data data.frame</dd>


<dt>color_dict</dt>
<dd>Named string featuring colors as values and labels (true labels) as names</dd>


<dt>show_x_label</dt>
<dd>A boolean, if `TRUE` the sample labels in the X axis will be shown. Default is `FALSE`.</dd>


<dt>base_size</dt>
<dd>An integer defining the base size of the text in the plot. Default is `14`.</dd>


<dt>...</dt>
<dd>Parameters passed to the ggplot2::theme function.</dd>

</dl>

deconvolution_barplot: Stacked barplot of deconvolution results

Description

Usage

Value

Arguments