gather_graph_node

Gather graph nodes from a data frame
Please note that this function is from the 'ggraph' package and has not been altered in functionality,
but it has been optimized and iterated.
It is not original content of 'TransProR'.
However, since 'ggraph' caused frequent GitHub Action errors during the creation of 'TransProR',
the author directly referenced the involved functions in 'TransProR'.
This is not the author's original creation. All users please be aware!

A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10.1186/s13059-022-02648-4>), providing flexible and robust approaches to RNA-Seq data analysis. For more information, refer to the package vignettes and related publications.

Dongyue Yu

TransProR

Analysis and Visualization of Multi-Omics Data

gather_graph_node function

<dl><dt>df</dt>
<dd>A data frame</dd>
<dt>index</dt>
<dd>A vector of column names to group by</dd>
<dt>value</dt>
<dd>Column name used for summarizing node size, defaults to the last column</dd>
<dt>root</dt>
<dd>Root name for the root node connections, optional</dd></dl>

Arguments

Gather graph nodes from a data frame
Please note that this function is from the 'ggraph' package and has not been altered in functionality,
but it has been optimized and iterated.
It is not original content of 'TransProR'.
However, since 'ggraph' caused frequent GitHub Action errors during the creation of 'TransProR',
the author directly referenced the involved functions in 'TransProR'.
This is not the author's original creation. All users please be aware! — gather_graph_node

<dl>

<dt>df</dt>
<dd>A data frame</dd>


<dt>index</dt>
<dd>A vector of column names to group by</dd>


<dt>value</dt>
<dd>Column name used for summarizing node size, defaults to the last column</dd>


<dt>root</dt>
<dd>Root name for the root node connections, optional</dd>

</dl>

Gather graph nodes from a data frame
Please note that this function is from the 'ggraph' package and has not been altered in functionality,
but it has been optimized and iterated.
It is not original content of 'TransProR'.
However, since 'ggraph' caused frequent GitHub Action errors during the creation of 'TransProR',
the author directly referenced the involved functions in 'TransProR'.
This is not the author's original creation. All users please be aware!

Description

Usage

Value

Arguments