Question about the dots on Quartile groups in boxplot
You add the points with geom_point(). Just remove it and you will get your "empty" boxplot. 

q &lt;- ggboxplot(B, x = "Type", y = "Gene",
               color = "black", palette = "npg",
               ylab = 'Gene expression', xlab=FALSE,
               order=c("Normal", "Tumor"))


Unfortunately I couldn't use stat_compare_means(method = "t.test") and     stat_n_text(), but this two just add the labels.