## Friday, September 13, 2013

### How to expand color palette with ggplot and RColorBrewer

Histograms and bar charts are almost always a part of data analysis presentation. If it is made with R ggplot package functions geom_histogram() or geom_bar() then bar chart may look like this:

The elegance of ggplot functions realizes in simple yet compact expression of visualization formula while hiding many options assumed by default. Hiding doesn't mean lacking as most options are just a step away. For example, for color color selection use one of the methods from the scale family of functions such as scale_fill_brewer():

And argument palette controls choice of colors in scale_fill_brewer():

Palettes used live in the package RColorBrewer - to see all available choices simply run display.brewer.all()

There are 3 types of palettes - sequential, diverging, and qualitative - each palette containing from 8 to 12 colors (see data frame brewer.pal.info or help ?RColorBrewer for more detail).

Curious reader may notice that if a bar chart contains 13 or more bars we get in trouble with colors like in the next plot:

Indeed length(unique(mtcars\$hp)) finds 22 unique values for the attribute horse power, while the palette Set2 has 8 colors to choose from. Lack of colors in the palette triggers ggplot to issue warning like this (and invalidates plot as seen above):
1: In brewer.pal(n, pal) :
n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors
RColorBrewer gives us a way to produce larger palettes by interpolating existing ones with constructor function colorRampPalette(). It generates a function that does actual job of build palettes with arbitrary number of colors by interpolating existing palette. Thus expanding the palette Set1 of 9 colors to 22 (the number of unique horse power values in mtcars):

While we addressed color palette deficiency other interesting things happened: even though all bars are back and are distinctly colored we lost the color legend. I intentionally added theme(legend.position=...) to showcase this fact: despite explicit position request in theme() the legend is no more part of the plot.

The difference: fill parameter was moved outside of histogram aes() function which effectively removed color information from ggplot() aesthetics mapping. Hence, there is nothing to apply legend to.

To fix move fill back into aes() and use scale_fill_manual() to define custom palette:

Another likely problem with large number of bars in plots like above is placing and layout of the legend. Adjust legend position and layout using theme() and guide_legend() functions as follows:

Finally, the same example using  in place palette constructor with different choice of library palette:

There are quite a few more scale functions to choose from depending on aesthetics type (colour, fill), color types (gradient, hue, etc.), data values (discrete or continuous).

UPDATE (09.16.17)
Not to undermine usefulness of RColorBrewer but there are more choices available in R. One example is package ggthemes that besides offering complete themes and scales for ggplot2 contains themed color palettes:

## Wednesday, July 31, 2013

### Quick R tip: ggplot in functions needs some extra care

When building visualizations with ggplot2 in R I decided to create specialized functions that encapsulate plotting logic for some of my creations. In this case instead of commonly used aes function I had to use its alternative -  aes_string - for aesthetic mapping from a string.

And now goes this handy tip:
while original aesthetic mapping function aes accepts x and y parameters by position:

p = ggplot(data, aes(x, y)) + ...

aes_string even though silently accepts them won't work like this:

my_plot_fun = function(data, xname, yname) {
p = ggplot(data, aes_string(xname, yname)) + ...
}

It will run to compile plot object without problems but when plot p (returned from the function my_plot_fun) executed this rather cryptic error appears:

Error in as.environment(where) : 'where' is missing

What it means is that ggplot never got aesthetics defined right. This is due to aes_string function lacking the same position parameters as in its aes counterpart above. Instead, define both x and y parameters (and others if necessary) by name:

p = ggplot(data, aes_string(x=xname, y=yname)) + ...

Created by Pretty R at inside-R.org

#### UPDATE:

One more vote for using aes_string in place of aes comes from CRAN submission policy, i.e.:
In principle, packages must pass R CMD check without warnings or significant notes to be admitted to the main CRAN package area. If there are warnings or notes you cannot eliminate (for example because you believe them to be spurious) send an explanatory note as part of your covering email, or as a comment on the submission form.
(source: CRAN Repository Policy)
What happens is that  R CMD check  reports notes like this for every aes call:

no visible binding for global variable [variable name]
It turns out that the most sensible solution is using aes_string instead.