publish_gostplot

This function allows to highlight a list of selected terms on the Manhattan plot created with the gprofiler2::gostplot() function.
The resulting plot is saved to a publication ready image if 'filename' is specified.
The plot is very similar to the one shown in the g:GOSt web tool after clicking on circles.

A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler/>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects.
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.

Liis Kolberg

gprofiler2

Interface to the 'g:Profiler' Toolset

publish_gostplot function

<dl><dt>p</dt>
<dd>ggplot object from gostplot(gostres, interactive = FALSE) function</dd>
<dt>highlight_terms</dt>
<dd>vector of selected term IDs from the analysis or a (subset) data.frame that has a column called 'term_id'. No annotation is added if set to NULL.</dd>
<dt>filename</dt>
<dd>file name to create on disk and save the annotated plot. Filename extension should be from c("png", "pdf", "jpeg", "tiff", "bmp").</dd>
<dt>width</dt>
<dd>plot width in inches. If not supplied, the size of current graphics device is used.</dd>
<dt>height</dt>
<dd>plot height in inches. If not supplied, the size of current graphics device is used.</dd></dl>

Arguments

Liis Kolberg &lt;liis.kolberg@ut.ee&gt;

Author

Create and save an annotated Manhattan plot of enrichment results. — publish_gostplot

<dl>

<dt>p</dt>
<dd>ggplot object from gostplot(gostres, interactive = FALSE) function</dd>


<dt>highlight_terms</dt>
<dd>vector of selected term IDs from the analysis or a (subset) data.frame that has a column called 'term_id'. No annotation is added if set to NULL.</dd>


<dt>filename</dt>
<dd>file name to create on disk and save the annotated plot. Filename extension should be from c("png", "pdf", "jpeg", "tiff", "bmp").</dd>


<dt>width</dt>
<dd>plot width in inches. If not supplied, the size of current graphics device is used.</dd>


<dt>height</dt>
<dd>plot height in inches. If not supplied, the size of current graphics device is used.</dd>

</dl>

publish_gostplot: Create and save an annotated Manhattan plot of enrichment results.

Description

Usage

Value

Arguments

Author

Examples