You need to tell ggplot to use shape=21 for the legend, so that it uses a point that pays attention to the fill specification, i.e.
scale_fill_manual(name=bquote(bold(paste(alpha, " "))),
values = cols,
guide=guide_legend(override.aes=list(shape=21))
Full example:
cols <- c("red","blue")
set.seed(101)
library(ggplot2)
mydata <- data.frame(ID=rep(c("KO", "WT"), each=4),
O=rep(c("HP", "NN"), each=2, times=2),
Methionine=rep(c("- Methionine", "+ Methionine"), each=2, times=2),
mean.1=sample(50:100, 8),
se.1=runif(8, min=1, max=3))
gg0 <- ggplot(mydata,
aes(x=O, y=mean.1, ymax=max(mean.1), shape=Methionine, fill=ID)) +
geom_errorbar(aes(ymin=mean.1-se.1, ymax=mean.1+se.1),
size=1,colour="black", width=.15) +
geom_point( size = 10)+
scale_shape_manual(labels=c("+ Methionine", "- Methionine"),
values = c(21,22))
gg0 +
scale_fill_manual(name=bquote(bold(paste(alpha, " "))),
values = cols,
guide=guide_legend(override.aes=list(shape=21))
