plot_pathways

Make a bubble plot of clean enriched pathways obtained from 'ConsensusPathDB' by performing gene set overexpression analysis. Colours represent the clusters to which each pathway belongs. You need to run the function <code>clean_pathways</code> to obtain the input data frame.

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_pathways function

<dl> <dt>final_df_pathway</dt>
<dd>Clean and clustered pathways obtained using clean_pathways.</dd> <dt>total_no_background_genes</dt>
<dd>Total no of genes in the background set.</dd> <dt>fontsize</dt>
<dd>Font size of the pathways to be displayed on y-axis.</dd></dl>

Arguments

Author

Plot clean enriched pathways as a bubble plot — plot_pathways

<dl>

 <dt>final_df_pathway</dt>
<dd>Clean and clustered pathways obtained using clean_pathways.</dd>

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

 <dt>fontsize</dt>
<dd>Font size of the pathways to be displayed on y-axis.</dd>

</dl>

plot_pathways: Plot clean enriched pathways as a bubble plot

Description

Usage

Value

Arguments

Author

See Also

Examples