plot_DGSA

It draws the heatmap of the DGSA result by selecting the 100 genes with
the highest variability between samples.

Mapper-based survival analysis with transcriptomics data is designed to carry out.
Mapper-based survival analysis is a modification of Progression Analysis of Disease (PAD)
where survival data is taken into account in the filtering function. More
details in: J. Fores-Martos, B. Suay-Garcia, R. Bosch-Romeu, M.C. Sanfeliu-Alonso,
A. Falco, J. Climent, "Progression Analysis of Disease with Survival (PAD-S) by SurvMap
identifies different prognostic subgroups of breast cancer in a large combined set of transcriptomics
and methylation studies" <doi:10.1101/2022.09.08.507080>.

Miriam Esteve

GSSTDA

Gene Structure Survival using Topological Data Analysis

Raquel Bosch

Jaume Forés

Joan Climent

Antonio Falco

plot_DGSA function

<dl><dt>selected_matrix_disease_component</dt>
<dd>Disease component matrix of
the selected genes that contains the disease component of all patients.
Output of the function <code>generate_disease_component</code>.</dd>
<dt>case_tag</dt>
<dd>Character vector of the same length as the number of
columns of full_data. Patients must be in the same order as in full_data.
It must be indicated for each patient whether he/she is healthy or not.
One value should be used to indicate whether the patient is healthy and
another value should be used to indicate whether the patient's sample is
tumourous. The user will then be asked which one indicates whether
the patient is healthy. Only two values are valid in the vector in total.</dd></dl>

Arguments

plot DGSA — plot_DGSA

<dl>

<dt>selected_matrix_disease_component</dt>
<dd>Disease component matrix of
the selected genes that contains the disease component of all patients.
Output of the function <code>generate_disease_component</code>.</dd>


<dt>case_tag</dt>
<dd>Character vector of the same length as the number of
columns of full_data. Patients must be in the same order as in full_data.
It must be indicated for each patient whether he/she is healthy or not.
One value should be used to indicate whether the patient is healthy and
another value should be used to indicate whether the patient's sample is
tumourous. The user will then be asked which one indicates whether
the patient is healthy. Only two values are valid in the vector in total.</dd>

</dl>

plot_DGSA: plot DGSA

Description

Usage

Value

Arguments