R & GGPLOT – Expanded Plots


Learn how to create expanded inserts like this easily in R with this ggplot template.

Learn how to create expanded inserts like this easily in R with this ggplot template.

>>GET THE R CODE<<

R and GGPLOT are great! There are some things, however, that I want to be able to do easily. For these things I have to create template codes, which I want to share with you!

This time around I wanted to show you how you can create “zoomed” areas of a plot and insert them into your main plot. This template will also show you how you can insert a completely different plot as an insert. This could be a table, map,….anything. This is a common thing to see in many plots, and alas now the functionality can be achieved easily.

DOWNLOAD TEMPLATE – Link to download from my script archive

Summary of the code:

  • You will define two plots: p1 and p2
    • p1 is the main plot – code it normally
    • p2 is the zoomed in area of p1 – the code for this is almost the same (see differences below)
    • p2 is placed inside of p1 and placed automatically into one of the corners that you specify
  • The differences between p1 and p2 are:
    • p1 has a rectangular grob defining the zoomed area – make sure the variables for its limits are linked to the customisation variables!
    • p2 has had the theme options changed to get rid of scales etc – we basically want the plot area to take up the entire device for p2, with no scales or padding.
  • Most of the customisation in the template is automated with variables – found at the top of the document
    • zoom – set the level of zoom
    • pad – set the padding of the insert
    • ex.col – fill colour of the expand boxes if you wish
    • ex.alpha – set this alpha to zero if you don’t want a fill
    • ex.lin – line colour of the zoom boxes
    • x.expand – the x range you wish to expand
    • y.expand – the y range you wish to expand
    • j.expand – the corner you wish the zoomed box to be in
    • ….other variables must be defined, but these are nicely laid out in a box at the top of the code
  • Awesome features of the code include
    • Aspect ratio is maintained for your zoomed area
    • Level of zoom can be easily defined – everything else is adjusted accordingly
    • The zoomed area is labeled with a zoom level
    • You can position the expanded box in any corner simply by defining j.expand as “tl” for Top Left etc – the computation of plotting coordinates is done automatically
    • Resolution is dynamic in the zoom box – so if you change your mind about zoom, it can be adjusted at 100% resolution – no loss

DOWNLOAD TEMPLATE – Link to download from my script archive

The code is easily customised, but pay attention to areas of code that are linked into customisation parameters. When you create your own code you should link in these variables into your plot to allow easy editing! To help you out with this, parts of the plot code that contain variables linked into the customisation parameters are commented with “#IMPORTANT“. As a general rule, though, follow this workflow:

  1. Create your base plot (p1)
  2. Define the rectangular grob (using customisation variables)
  3. Copy and use theme () options from p1 in the template
  4. Duplicate p1 to create p2
  5. Copy and use the theme () options for p2 from the template

If you have any questions, please don’t hesitate to comment. If you are having problems, provide simple examples of code which exhibit the problem you’re having and I’ll do my best to look at it!

Below are some edits of the code that show you how easily things can be changed…

zoom = 2.6

zoom = 2.6

pad = 3Screen Shot 2013-11-26 at 19.26.38

ex.lin = “red”

Screen Shot 2013-11-26 at 19.28.04

zoom = 5; pad = 1; x.expand = c(3, 4); y.expand = c(13, 16), j.expand = “br”

Screen Shot 2013-11-26 at 19.33.19

#14 A New GGPLOT Template


Screen Shot 2013-02-13 at 10.46.11

 

So the opts() has now been given the boot, and all the cool kids are using theme() to customise their ggplots. If you’re still on an old version of R then theme() will still work, but if you update (which you should) then it’ll stop working and you’ll have to edit all your code which uses theme ().

Here is my standard template giving you a style for simple, publication friendly ggplot plots.

# Load Packages
library (ggplot2) # Needed for plotting
library (grid) # Needed for customising plot area
library (scales) # Needed for ediring log tickmarks

# Select Font Size
size1 = 20 # Plot and Axis Titles
size2 = 17 # Legend Title
size3 = 15 # Axis Labels

ggplot (
     data = mtcars,
     aes (
     x= disp,
     y= drat
     )
     ) +

geom_point (
     aes(
     colour = mpg
     ),
     size = 5
     ) +

scale_y_log10 (
     limits = c(0.01, 10),
     name = "Axis Title Here",
     label = trans_format('log10',math_format(10^.x)) # Format = 10^x rather than 1e10x (also use label = comma)
     ) +

scale_x_log10 (
      limits = c(10, 1000),
     name = "Axis Title Here",
     label = trans_format('log10',math_format(10^.x)) # Format = 10^x rather than 1e10x (also use label = comma)
     ) +

annotation_logticks ( # Turn on minor ticks
     short = unit (0.2, "cm"), # Minor tick length
     mid = unit (0.2, "cm"), # ...
     long = unit (0.2, "cm"), # ...
     side = "lbrt") + # l = left, b = bottom etc

labs ( # New way of setting some attributes.
     colour = "MPG",
     title = "Plot Title"
     ) +

theme (
      plot.title = element_text (vjust = 3, size = 20), # plot title attrib.
      plot.margin = unit (c(3, 3, 3, 3), "lines"), # plot margins
      panel.border = element_rect (colour = "black", fill = F, size = 1), # axis colour = black
      panel.grid.major = element_blank (), # remove major grid
      panel.grid.minor = element_blank (), # remove minor grid
      panel.background = element_rect (fill = "white"), # background colour
      legend.background = element_rect (fill = "white"), # background colour
      legend.justification=c(0, 0), # lock point for legend
      legend.position = c(0, 0), # put the legend INSIDE the plot area
      legend.key = element_blank (), # switch off the rectangle around symbols in the legend
      legend.title = element_blank (), # switch off the legend title
      legend.text = element_text (size = 15), # sets the attributes of the legend text
      axis.title.x = element_text (vjust = -2, size = 20), # change the axis title
      axis.title.y = element_text (vjust = -0.1, angle = 90, size = 20), # change the axis title
      axis.text.x = element_text (size = 17, vjust = -0.25, colour = "black"),# change the axis label font attributes
      axis.text.y = element_text (size = 17, hjust = 1, colour = "black"), # change the axis label font attributes
      axis.ticks = element_line (colour = "black", size = 0.5), # sets the thickness and colour of axis ticks
      axis.ticks.length = unit(-0.25 , "cm"), # -ve length = inside ticks
      axis.ticks.margin = unit(0.5, "cm") # margin between the ticks and the text
      )