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const-ae / ggsignif

Easily add significance brackets to your ggplots
https://const-ae.github.io/ggsignif/
GNU General Public License v3.0
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FDR warning #134

Closed mlkleinbest closed 4 months ago

mlkleinbest commented 4 months ago

The following code was working, now it's returning a warning, "Warning: Ignoring unknown parameters: FDR"

plotmeth0<-ggplot(data = dat.agr.meth, aes(x = Treatment, y=Abundance)) +
  geom_boxplot(outlier.shape = NA) +
  geom_jitter(aes(color = Genus), height = 0, width = .2) +
  labs(x = "", y = "Relative Abundance\n") + facet_wrap(~Genus, scales = "free", ncol=3)+theme(axis.text.x = element_text(angle = 90))+theme_bw()+ggtitle("Day 0")+
  geom_signif(test='wilcox.test',FDR=TRUE, comparisons = split(t(combn(comp, 2)), seq(nrow(t(combn(comp, 2))))),
  map_signif_level = F, textsize = 4, step_increase = 0.1,vjust = 1.9)

print(plotmeth0)
IndrajeetPatil commented 4 months ago

That's because there is no such parameter for geom_signif().

If you are wondering about how to apply FDR-correction, it is currently not supported: https://github.com/const-ae/ggsignif/issues/28