pub_activity_plot

This function uses three input parameters, one gene list, one defined set of keywords and
species, to run a PubMed database search, and returns an annotated overview of a publication
activity plot.

Visualising publication activity per gene based on a gene list and a user-defined set of keywords utilising R 'rentrez' <https://cran.r-project.org/package=rentrez/> that provides 'NCBI' <https://www.ncbi.nlm.nih.gov> database search like in 'PubMed' <https://pubmed.ncbi.nlm.nih.gov>. It summarises the retrieved number of publications for each gene in an overview bar plot (saved as 'png' file) and by choice a summary table (as 'csv') that including the most recent 100 'PubMed' IDs and publication titles.

Marina Leer

GeSciLiVis

Gene-Based Publication Activity Visualiser

George Soultoukis

Masoome Oveisi

German Research Foundation 

German Ministry of Education and Research  

State of Brandenburg 

pub_activity_plot function

<dl><dt>g_list</dt>
<dd>list of official gene symbols &lt;= 30 elements.</dd>
<dt>k_list</dt>
<dd>list of keywords &lt;= 10 elements.</dd>
<dt>species</dt>
<dd>selecting the species of interest (species="mouse" or species="human").</dd>
<dt>output_dir</dt>
<dd>path to output directory to save resulting csv and png, NULL for not saving.</dd>
<dt>show_progressbar</dt>
<dd>boolean: whether to show progress bar</dd></dl>

Arguments

Visualize the publication activity for genes — pub_activity_plot

<dl>

<dt>g_list</dt>
<dd>list of official gene symbols &lt;= 30 elements.</dd>


<dt>k_list</dt>
<dd>list of keywords &lt;= 10 elements.</dd>


<dt>species</dt>
<dd>selecting the species of interest (species="mouse" or species="human").</dd>


<dt>output_dir</dt>
<dd>path to output directory to save resulting csv and png, NULL for not saving.</dd>


<dt>show_progressbar</dt>
<dd>boolean: whether to show progress bar</dd>

</dl>

pub_activity_plot: Visualize the publication activity for genes

Description

Usage

Value

Arguments

Examples