An example of using a named color vector to set colors in ggplot2

named_color_vector.r

# The incantation
options(stringsAsFactors = FALSE)

library(ggplot2)


# Some sample data
# A test that can result in a negative or positive only
testres2 <- data.frame(result = c("Negative", "Positive"),
                       n = c(850, 150)
)

# A different test that has a borderline result
testres3 <- data.frame(result = c("Negative", "Positive", "Borderline"),
                      n = c(700, 270, 30)
)


# I want to use the same color scale for both tests, even though 
# they have different result sets
# Red, green, blue
resultcolors <- c("#1F78B4", "#F03B20", "#31A354")

# In this case, ggplot2 just uses the first two colors in the vector
ggplot(testres2, aes(x = result, weight = n, fill = result)) +
    geom_bar() +
    scale_fill_manual("Result", values = resultcolors)

# Here it uses all three - assigning them to results in the
# order they appear in the data
ggplot(testres3, aes(x = result, weight = n, fill = result)) +
    geom_bar() +
    scale_fill_manual("Result", values = resultcolors)


# So if I change the order the results appear in for whatever
# reason, my color scheme is hosed
ggplot(testres3[order(testres3$result), ], aes(x = result, weight = n, fill = result)) +
    geom_bar() +
    scale_fill_manual("Result", values = resultcolors)


# I want negative to be red, positive to be blue, and 
# indeterminate to be green - everywhere, and without regard
# to the order of the data.frame 

# Using a named vector instead...
namedcolors <- resultcolors
names(namedcolors) <- c("Positive", "Negative", "Borderline")

# Even though only two colors are in use, this plot correctly uses
# red and blue
ggplot(testres2, aes(x = result, weight = n, fill = result)) +
    geom_bar() +
    scale_fill_manual("Result", values = namedcolors)

# Same here
ggplot(testres3, aes(x = result, weight = n, fill = result)) +
    geom_bar() +
    scale_fill_manual("Result", values = namedcolors)


# Order of values in data doesn't matter
ggplot(testres3[order(testres3$result), ], 
    aes(x = result, weight = n, fill = result)) +
    geom_bar() +
    scale_fill_manual("Result", values = namedcolors)

# Even if I put my thang down, flip it and reverse it
ggplot(testres3[order(testres3$result, decreasing = TRUE), ], 
    aes(x = result, weight = n, fill = result)) +
    geom_bar() +
    scale_fill_manual("Result", values = namedcolors)

This was the answer to something I have been trying to figure out for 2 hours. Thanks for this!