Column colors not matching custom scale - ggplot2

Question

I've put together a barplot that gives counts for phenotypes in the maxilla and mandible. I'd like the maxilla bars to be in black, and the mandible in grey. I've created a scale color variable for the fill option, yet not luck, the colors are still out of order.
I've already used this code successfully on a number of other barplots, but no luck here. I believe it is because I have combined 3 data frames into one using rbind, however the structure of the combined data frame is no different from the uncombined one, which do work.
The first four bars should be black, the last four bars should be grey.
### 3 data sets
a<-data.frame(
row.names = c("RI2_MAX_E1","ri2_mand_E1","rc1_mand_E1"),
count = c(2,2,2),
labels = c("RI2", "ri2", "rc1")
)
b<-data.frame(
row.names = c("RP3_MAX_E1","RP4_MAX_E1","rp3_mand_E1"),
count = c(3,3,2),
labels = c("RP3", "RP4", "rp3")
)
c<-data.frame(
row.names = c("RM3_MAX_E1","rm3_mand_E1"),
count = c(5,6),
labels = c("RM3", "rm3")
)
### Bind datasets into 1
E1.bind<-rbind(a,b,c)
### order variables
E1.bind$labels<-factor(E1.bind$labels, levels =c("RI2","RP3","RP4","RM3","ri2","rc1","rp3","rm3"))
### Custom scale color
E1.color<-c("black","black","black","black","grey","grey","grey","grey")
### plot
ggplot(data= E1.bind, aes(x=E1.bind$labels, y=E1.bind$count,fill=E1.color)) +
geom_bar(stat="identity") +
xlab("Teeth") + ylab("Phenotype counts") +
ggtitle("Teeth With Greatest Number of Phenotypes - Element 1")+
scale_fill_manual(name="",
labels = c("Maxilla","Mandible"),
values = c("black","grey"))+
scale_x_discrete(labels = c("RI2","RP3","RP4","RM3","ri2","rc1","rp3","rm3")) +
scale_y_continuous(breaks = seq(0,6,1)) +
theme_classic()+
theme(legend.position="top")+
theme(plot.title = element_text(hjust = 0.5))

Answer 1

Your E1.bind looks like this:
E1.bind
count labels
RI2_MAX_E1 2 RI2
ri2_mand_E1 2 ri2
rc1_mand_E1 2 rc1
RP3_MAX_E1 3 RP3
RP4_MAX_E1 3 RP4
rp3_mand_E1 2 rp3
RM3_MAX_E1 5 RM3
rm3_mand_E1 6 rm3
Note the order of the labels. Then you are using this as fill:
E1.color<-c("black","black","black","black","grey","grey","grey","grey")
A better way is to add a Type to your dataframe that you use to define the fill color. That way it's also more scalable:
library(dplyr)
library(ggplot2)
a<-data.frame(
row.names = c("RI2_MAX_E1","ri2_mand_E1","rc1_mand_E1"),
count = c(2,2,2),
labels = c("RI2", "ri2", "rc1")
)
b<-data.frame(
row.names = c("RP3_MAX_E1","RP4_MAX_E1","rp3_mand_E1"),
count = c(3,3,2),
labels = c("RP3", "RP4", "rp3")
)
c<-data.frame(
row.names = c("RM3_MAX_E1","rm3_mand_E1"),
count = c(5,6),
labels = c("RM3", "rm3")
)
### Bind datasets into 1
E1.bind<-rbind(a,b,c)
E1.bind$Type <- ifelse(grepl('R.*', E1.bind$labels), "Maxilla", "Mandible")
### Sort by Type
E1.bind <- arrange(E1.bind, desc(Type))
### plot
ggplot(data= E1.bind, aes(x=labels, y=count, fill=Type)) +
geom_bar(stat="identity") +
xlab("Teeth") + ylab("Phenotype counts") +
ggtitle("Teeth With Greatest Number of Phenotypes - Element 1") +
scale_y_continuous(breaks = seq(0,6,1)) +
scale_x_discrete(limits=E1.bind$labels) +
scale_fill_manual(values = c("grey", "black")) +
theme_classic()+
theme(legend.position="top")+
theme(plot.title = element_text(hjust = 0.5))
This results in: