I am having an issue with the ggplot code line where R doesn't like the "group = Year".
Here is what my data looks like:
> head(data.scores.pa)
NMDS1 NMDS2 NMDS3 Site Year Elevation Fire history
1 -0.737547 0.73473457 0.7575643 BF 2004 1710 Burnt
......
> head(spp.scrs2)
species MDS1 MDS2 pval
1 Acrothamnus.montanus 0.8383 -0.02382347 1e-04
........
> head(vec.sp.df.pa)
MDS1 MDS2 species pvals
Elevation 0.834847 0.747474 Elevation 0.005
Here is the code I am using:
>xy <- ggplot(data.scores.pa, aes(x = NMDS1, y = NMDS2, group = Year)) +
geom_point(size = 3, aes(shape = Fire history, colour = Year))+
stat_ellipse(mapping = NULL, data = NULL, geom = "path", position = "identity", type = "t", level = 0.95, segments = 51, na.rm = FALSE, show.legend = NA, inherit.aes = TRUE) +
geom_segment(data=vec.sp.df.pa, aes(x=0,xend=MDS1,y=0,yend=MDS2),
arrow = arrow(length = unit(0.5,"cm")),colour="grey")+
geom_text_repel(data=vec.sp.df.pa,aes(x=MDS1,y=MDS2,label=species),size=2)+
geom_segment(data=spp.scrs2,aes(x=0,xend=MDS1,y=0,yend=MDS2),
arrow = arrow(length = unit(0.5, "cm")),colour="black")+
geom_text_repel(data=spp.scrs2, aes(x=MDS1,y=MDS2,label=species),size=2)+
annotate("text", x = -1.6, y = 1, label = paste0("3D stress: ", format(ord.pa$stress, digits = 4)), hjust = 0) +
theme_cowplot() + scale_color_brewer(palette = "BrBG", direction = 1) +
theme(panel.border = element_rect(colour = "black"))+
ggtitle("All Sites - distance data using Bray-Curtis")+
labs(x = "NMDS1", y = "NMDS2")
> Error in FUN(X[[i]], ...) : object 'Year' not found
However, when I remove the geom_segment and geom_text_repel code lines it fixes the problem and I am able to plot the graph...
Is anyone able to provide some insight into this issue?
Thank you!