PlotEnrichedPathways

This function is used to generate a combined plot for the enriched pathways from KEGG and REACTOME

Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.

Mohamed Soudy

UniprotR

Retrieving Information of Proteins from Uniprot

Ali Mostafa

PlotEnrichedPathways function

<dl><dt>Accs</dt>
<dd>Vector of UniProt Accession/s or genes</dd>
<dt>OS</dt>
<dd>organism name Example: human - 'hsapiens', mouse - 'mmusculus'</dd>
<dt>p_value</dt>
<dd>custom p-value threshold for significance, default = 0.05</dd>
<dt>Path</dt>
<dd>Path to save output plot</dd>
<dt>theme</dt>
<dd>optional parameter to generate specific theme for journals ex: "aaas", "nature", "lancet", "jama"</dd>
<dt>w</dt>
<dd>width of the generated plot</dd>
<dt>h</dt>
<dd>height of the generated plot</dd></dl>

Arguments

Mohmed Soudy <a href="/link/Mohamed.soudy%4057357.com?package=UniprotR&version=2.3.0" data-mini-rdoc="UniprotR::Mohamed.soudy@57357.com">Mohamed.soudy@57357.com</a> and Ali Mostafa <a href="/link/ali.mo.anwar%40std.agr.cu.edu.eg?package=UniprotR&version=2.3.0" data-mini-rdoc="UniprotR::ali.mo.anwar@std.agr.cu.edu.eg">ali.mo.anwar@std.agr.cu.edu.eg</a>

Author

Connect and parse UniProt information — PlotEnrichedPathways

<dl>

<dt>Accs</dt>
<dd>Vector of UniProt Accession/s or genes</dd>


<dt>OS</dt>
<dd>organism name Example: human - 'hsapiens', mouse - 'mmusculus'</dd>


<dt>p_value</dt>
<dd>custom p-value threshold for significance, default = 0.05</dd>


<dt>Path</dt>
<dd>Path to save output plot</dd>


<dt>theme</dt>
<dd>optional parameter to generate specific theme for journals ex: "aaas", "nature", "lancet", "jama"</dd>


<dt>w</dt>
<dd>width of the generated plot</dd>


<dt>h</dt>
<dd>height of the generated plot</dd>

</dl>

Mohmed Soudy <a href='mailto:Mohamed.soudy@57357.com'>Mohamed.soudy@57357.com</a> and Ali Mostafa <a href='mailto:ali.mo.anwar@std.agr.cu.edu.eg'>ali.mo.anwar@std.agr.cu.edu.eg</a>

PlotEnrichedPathways: Connect and parse UniProt information

Description

Usage

Arguments

Author