Closed Elseedy28 closed 1 year ago
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
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![canonical_Wnt_signaling_pathway](https://user-images.githubusercontent.com/115556489/196208328-dc7f9925-f81a-46e1-bd84-0c2202197083.png)
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