Is it possible to increase the gene label size in Combined Results Graph?

[fengx90]

Hello Ege,

Thanks very much for developing a great package for the community!
When I plot the enriched terms, the labeling of genes and term descriptions are quite small. Is there a way to increase the labeling size for better output figure quality? Thanks very much!

Best,
Feng

[YunielFM]

Hi Feng, the answer is quite easy. The results from the enrichment plots are actually ggplots. This mean that you can manually customize most of them. Example:

1. Create the bubble chart from your pathfindR result, in this case, show 40 pathways.
   p <- enrichment_chart(pathwaysT1, top_terms = 40)

2. Now you can customize everything in the ggplot object, in this case, I am reducing the size of the text on the y-axis to accommodate all the labels. You would need to do the opposite.
   p + theme(axis.text.y = element_text(size = 7))

Happy plotting, and indeed, the package rocks!

[YunielFM]

For the sake of completeness, if you were referring to the network plots, the text size adjustment is a bit tricky but doable. You basically need to hack into the function and add the text size you want for each gene in the plot.
Just type in your console combined_results_graph. Copy the output and create a customized function , smth like my.combined.plot <- function (combined_df, selected_terms = "common",........... Then, in your function change the line:
p <- p + suppressWarnings(ggraph::geom_node_text(ggplot2::aes_(label = ~name), nudge_y = 0.2, repel = TRUE, max.overlaps = 20))
to:
p <- p + suppressWarnings(ggraph::geom_node_text(ggplot2::aes_(label = ~name), size = 3, color = "grey0", nudge_y = 0.2, repel = TRUE, max.overlaps = 20))
Notice I also changed the text color label. Probably there is another way, but this will solve your issue.
Of course, use your function to create the network plot!!

[fengx90]

Thanks very much for the reply! This is actually what I want, not to change the axis text size. Gonna try out!

[fengx90]

Just tried and it works! Thanks again! Really appreciated it!

[YunielFM]

Excellent!