deconv_pred_obs_plot

Produces one plot panel per number of methods with predictions. Each plot panel has one plot per cell type.

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

deconv_pred_obs_plot function

<dl><dt>deconv_df</dt>
<dd>A data.frame with meta.data, true values and predictions for different methods as columns. Each row should be a prediction for a given sample and a given group/cell type.</dd>
<dt>true_values_col</dt>
<dd>A string with the name of the column with the true values in `deconv_df`.</dd>
<dt>predicted_cols</dt>
<dd>A vector of strings with the name of the columns with the predictions for different methods in `deconv_df`.</dd>
<dt>sample_id_col</dt>
<dd>A string with the name of the column with the sample name or ID in `deconv_df`.</dd>
<dt>group_col</dt>
<dd>A string with the name of the column containing the cell types or groups in `deconv_df`.</dd>
<dt>axis_lims</dt>
<dd>A list with two entries, `x` and `y`, defining the limits of the x and y axis of the plot.</dd></dl>

Arguments

Scatter plots of observed (true) vs predicted values for deconvolution. — deconv_pred_obs_plot

<dl>

<dt>deconv_df</dt>
<dd>A data.frame with meta.data, true values and predictions for different methods as columns. Each row should be a prediction for a given sample and a given group/cell type.</dd>


<dt>true_values_col</dt>
<dd>A string with the name of the column with the true values in `deconv_df`.</dd>


<dt>predicted_cols</dt>
<dd>A vector of strings with the name of the columns with the predictions for different methods in `deconv_df`.</dd>


<dt>sample_id_col</dt>
<dd>A string with the name of the column with the sample name or ID in `deconv_df`.</dd>


<dt>group_col</dt>
<dd>A string with the name of the column containing the cell types or groups in `deconv_df`.</dd>


<dt>axis_lims</dt>
<dd>A list with two entries, `x` and `y`, defining the limits of the x and y axis of the plot.</dd>

</dl>

deconv_pred_obs_plot: Scatter plots of observed (true) vs predicted values for deconvolution.

Description

Usage

Value

Arguments