ggplot2 : Volcano Plot. Weird connecting lines are appearing

Question

[VenGeno]

Hi,

I am using ggplot2 to visualize a differentially expressed gene set generated using ballgown. When I visualize it I see these weird connecting lines (blue) and small blue and tiny red dots. Link to the image :
I don't understand why it is happening. Following is the code I used,

options(ggrepel.max.overlaps = Inf)
ggplot(data=results_genes[results_genes$diffexpressed != "No",], aes(x=de, y=-log10(pval), label=gene_label, color = diffexpressed)) +
  xlab("log2Foldchange") +
  scale_color_manual(name = "Differentially expressed", values=c("blue", "red")) +
  geom_point() +
  theme_minimal() +
  geom_text_repel() +
  geom_vline(xintercept=c(-1, 1), col="red") +
  geom_hline(yintercept=-log10(0.05), col="red") +
  guides(colour = guide_legend(override.aes = list(size=5))) +
  geom_point(data = results_genes[results_genes$diffexpressed == "No",], aes(x=de, y=-log10(pval)), colour = "black")

Thank you in advance.

[cpad0112]

change the geom_text_repel to geom_text_repel(size = 4). Adjust the font size as per the graph.

Answer 1

[Matthias Zepper]

Maybe try without the geom_text_repel() layer?

I would suppose those small blue and red dots are in reality tiny gene name labels and the connecting lines the lines that connect the actual position with the label.

[VenGeno]

It wokred. Thank you Matthias Zepper !🙏

[Matthias Zepper]

You are welcome! Good luck with your analysis!