plot_go_terms

Make a bubble plot for significantly enriched Gene Ontologies (GO) Terms obtained after performing gene set overexpression analysis using 'ConsensusPathDB'.

Provides functions to have visualization and clean-up of enriched gene ontologies (GO) terms,
protein complexes and pathways (obtained from multiple databases) using 'ConsensusPathDB'
from gene set over-expression analysis. Performs clustering of pathway based on similarity
of over-expressed gene sets and visualizations similar to Ingenuity Pathway Analysis (IPA)
when up and down regulated genes are known. The methods are described in a paper currently
submitted by Orecchioni et al, 2020 in Nanoscale.

Raghvendra Mall

func2vis

Clean and Visualize Over Expression Results from
'ConsensusPathDB'

plot_go_terms function

<dl> <dt>df_goterms</dt>
<dd>The tab-separated data frame with the GO terms information obtained after performing gene set overexpression analysis using 'ConsensusPathDB'.</dd> <dt>total_no_background_genes</dt>
<dd>Total no of genes in the background set.</dd> <dt>negative_log_10_p_value_cutoff</dt>
<dd>The threshold on -log10(pvalue) to be used to identify the GO terms to be highlighted in the plot.</dd> <dt>max_overlap</dt>
<dd>To prevent overlapping text, set this paramater to a number &gt;= 20.</dd></dl>

Arguments

Author

Bupple Plot for GO Terms — plot_go_terms

<dl>

 <dt>df_goterms</dt>
<dd>The tab-separated data frame with the GO terms information obtained after performing gene set overexpression analysis using 'ConsensusPathDB'.</dd>

 <dt>total_no_background_genes</dt>
<dd>Total no of genes in the background set.</dd>

 <dt>negative_log_10_p_value_cutoff</dt>
<dd>The threshold on -log10(pvalue) to be used to identify the GO terms to be highlighted in the plot.</dd>

 <dt>max_overlap</dt>
<dd>To prevent overlapping text, set this paramater to a number &gt;= 20.</dd>

</dl>

plot_go_terms: Bupple Plot for GO Terms

Description

Usage

Value

Arguments

Author

Details

Examples