GSEA hallmark visualization

Question

[Rob]

Hi friends

I want to visualize hallmarks from GSEA.

I use this code:

p <- ggplot(data, aes(NES, reorder(HALLMARK, NES)))
p + geom_point(aes(colour=Significance, size = 0.5)) +
  scale_color_viridis(limits=c(0, 0.2)) +
  geom_vline(xintercept=0, size=1,colour="gray50") +
  theme(axis.text.y = element_text(size = 10),
        axis.line = element_line(linetype = "solid"),
        panel.background=element_rect(fill="white", colour="black", linetype = 'solid'),
        panel.grid.major=element_line(size=0.15,linetype='solid', colour="gray90"),
        panel.grid.minor=element_blank(),
        axis.title.y=element_blank(),
        axis.title.x = element_text(size = 14),
        legend.text = element_text(size=10)) +
  labs(title = "GSEA-Validation Set : Male", x = "NES", y = NULL, size = NULL, color = "FDR")

NES is normalized enrichment score; significance is FDR value

This is the resulted dot diagram:

How can I change the size and shape of dots to rectangle of triangle?

Also, is there other way to visualize the hallmarks?

[seidel]

You can choose your plot symbol using scale_shape_manual(values=17). geom_point() also has a shape attribute: geom_point(shape = 17). In R, the triangle shapes are: 2, 6, 17, 24, 25.

[Rob]

Thanks seidel How can I keep some as rectangel and some as circle and have a label for this in front of the diagram :circle:male; rectangel : female?