How to label the points on the graph itself using plot_gsva_pca()?

[levinhein]

What is the parameter in order to label the points inside the graph itself? It's hard to distinguish colors when there are too many data points. Adding "label = TRUE" seems not to be the right way to do it.

plot_gsva_pca(gsva_result)

[jgriss]

Hi @levinhein,

Thanks a lot for your interest in ReactomeGSA!

You can do this quite easily using standard ggplot2 functions. The following code adds labels on top of the points:

# After you received your GSVA result
plot_gsva_pca(gsva_result) + 
    geom_text(aes(label=sample), 
         nudge_x = 0.005, 
         nudge_y = 0.005, 
         check_overlap = T)

You'll probably have to adapt nudge_x and nudge_y to your result since it's based on the arbitrary PCA units.

Kind regards,
Johannes