Visualization

[Elseedy28]

Hello , i have a problem concerning the visualization method . i cannot have the bubble plot for the 10 enriched pathway and also when i have the PPi network it is not well labelled as term gene graph in your pipeline attached an example

and this is the code i am using there is no bug or error but i don't get any graph enrichment_chart(final_res[1:10, ]) term_gene_graph(final_res[1:10, ]) score_terms(final_res[1:10,])

Thanks heba

[egeulgen]

hello heba,

that is not the output of term_gene_graph(), it's the output visualize_term_interactions() and you can remove the legend by setting show_legend=FALSE either in visualize_term_interactions() or (better) visualize_terms().

enrichment_chart(final_res[1:10, ]) term_gene_graph(final_res[1:10, ])

The output of these are ggplot2 objects and are automatically displayed in the Plots console (if you are not using an IDE, assign the output to a variable, e.g., g <- enrichment_chart(final_res[1:10, ]) and you can save the plot by ggplot2::ggsave()

For score_terms(), you need the experiment (expression/methylation) matrix as another input.

Hope this helps, -E