Can I adjust the lower limit of scale_color_brewer?

Question

I have ordered categorical data that I would like to use color brewer on. But I have a hard time seeing the very light lower values. Is there a way to either trim off those lower values or set the lower limit in the scale?

ggplot(data.frame(x=1:6, y=10:15, w=letters[1:6]), aes(x, y, color=w)) + 
geom_point()+ scale_color_brewer(type="seq", palette=1) + theme_bw()

Is there a better way to do this? So far I either see qualitative scales that aren't ordered or continuous scales that don't like being applied to discrete data. I'm aware of manual scales if that's the only route.

Blindstory

A simple possible alternative would be to use a plot symbol which have an outline around a filled area, such as pch = 21 (see e.g. here). Then you could use the fill aesthetic instead. ggplot(data.frame(x = 1:6, y = 10:15, w = letters[1:6]), aes(x, y, fill = w)) + geom_point(pch = 21,size = 5)+ scale_fill_brewer(type = "seq", palette = 1) + theme_bw() – Feeble

Answer 1

You cannot just set a lower limit. But you can use a palette with more colors than needed and map the brightest colors to unused levels. Below is an example with 9 levels:

ggplot(data.frame(x=1:6, y=10:15, w=letters[1:6]), aes(x, y, color=w)) + 
  geom_point() + theme_bw() + 
  scale_color_brewer(type="seq", palette=1, 
                     limits=c(LETTERS[1:3], letters[1:6]), 
                     breaks=letters[1:6])

Sp

Yes! That's the workaround I was trying to figure out. Thanks! – Blindstory

Can you please elaborate on what you're doing in the limits argument here? Where does the all-caps LETTERS come from? How can this be extrapolated to a generic sense where I'm not plotting letters? – Hawking

Answer 2

While @shadow's answer was a start for me, the kind of brewer palette I needed to use (sequential) only has 9 values -- I had 8 categorical variables to plot! Removing only the 9th and lightest palette color still wasn't enough to make the color scheme completely visible.

So I used the colorRampPalette() function, which allows you to expand existing color palettes into continuous functions:

library(RColorBrewer)
ggplot(data.frame(x=1:6, y=10:15, w=letters[1:6]), aes(x, y, color=w)) + 
  geom_point() + theme_bw() + 
  scale_color_manual(values = colorRampPalette(brewer.pal(9, "YlGnBu"))(12)[6:12])

So in this case, I'm mapping the (maximum) 9 native colors from the "YlGnBu" palette onto 12 colors, and then only using the darkest 6 of those colors ([6:12]) in the plot.

Hawking

Answer 3

I'm not aware of any additional arguments you could pass to scale_colour_brewer() to set the lower limit of the scale (see http://docs.ggplot2.org/current/scale_brewer.html)

You have more flexibility with one of ggplot's colour options, which take the format of: scale_xxx_yyy, for example scale_fill_discrete() which take more arguments. See for example http://docs.ggplot2.org/current/scale_hue.html but also note the other options ('see also').

scale_fill_continuous might be a good starting place for ordinal data as you've requested.

You could, for example, pass colours from http://colorbrewer2.org/ to it, and choose a more suitable starting colour. The only problem is you would need to convert the rgb/hex values to HSL values using a tool such as: http://serennu.com/colour/hsltorgb.php

Helvetian

Thanks @Phil. I tried scale_colour_discrete but couldn't find a way to do ordered categorical values (ie on some sort of gradient). Do you know of a way? If I just pick values, then I'm pretty much back to manual. – Blindstory

I've updated my answer. @Sp 's answer was more applicable to your specific requirements, but the scale_xxx_yyy options are always worth considering. – Helvetian