My traditional work flow for embedding R graphics into a blog post has been via a PNG files that I upload online. However, when I created a ‘simple’ graphic with only basic curves and triangles for a recent post, I noticed that the PNG output didn’t look as crisp as I expected it to be. So, eventually I used a SVG (scalable vector graphic) instead.
Creating a SVG file with R could’t be easier; e.
I like the Economist theme in the latticeExtra package. It produces nice looking charts that mimic the design of the weekly newspaper, such as in this example:
For some time I wondered how I could put the title of my lattice plots into the top left corner as well (by default titles are centred). Reviewing the code of the theEconomist.theme function by Felix Andrews reveals the trick. It is the setting of par.
The forthcoming R Journal has an interesting article on the showtext package by Yixuan Qiu. The package allows me to use system and web fonts directly in R plots, reminding me a little of the approach taken by XeLaTeX. But “unlike other methods to embed fonts into graphics, showtext converts text into raster images or polygons, and then adds them to the plot canvas. This method produces platform-independent image files that do not rely on the fonts that create them.
Last week I mentioned the grid.arrange function of the gridExtra package that allows me to combine graphical grid objects onto one page. The latticeExtra package provides another elegant solution for trellis (lattice) plots: the function c.trellis() or just c() combines the panels of multiple trellis objects into one.
Here is minimal example from the help file of c.trellis:
library(latticeExtra) ## Combine different types of plots. c(wireframe(volcano), contourplot(volcano)) In my next example I am using data from Eurostat, the statistical office of the European Union, showing the use of public transport in four countries.
Occasionally I’d like to plot a table alongside a chart in R, e.g. to present summary statistics of the graph itself. Thanks to the gridExtra package this is quite straightforward. The function tableGrob creates a table like plot of a data frame, while arrangeGrob allows me to arrange ggplot2, lattice and grid graphical objects (short ‘grobs’, such as tableGrob) on a page.
Here is a little example: Session Info R version 3.
I love interactive pivot tables. That is the number one reason why I keep using spreadsheet software. The ability to look at data quickly in lots of different ways, without a single line of code helps me to get an understanding of the data really fast.
Perhaps I can do the same now in R as well. At yesterday’s LondonR meeting Enzo Martoglio presented briefly his rpivotTable package. Enzo builds on Nicolas Kruchten’s PivotTable.
Last week Arthur Charpentier sketched out a Markov spatial process to generate hurricane trajectories. Here, I would like to take another look at the data Arthur used, but focus on its time component.
According to the Insurance Information Institute, a normal season, based on averages from 1980 to 2010, has 12 named storms, six hurricanes and three major hurricanes. The usual peak months of August and September passed without any major catastrophes this year, but the Atlantic hurricane season is not over yet.
How did I miss the GrapheR package?
The author, Maxime Hervé, published an article about the package [1] in the same issue of the R Journal as we did on googleVis. Yet, it took me a package update notification on CRANbeeries to look into GrapheR in more detail - 3 years later! And what a wonderful gem GrapheR is.
The package provides a graphical user interface for creating base charts in R.
This post will present the wonderful pairs.panels function of the psych package [1] that I discovered recently to visualise multivariate random numbers.
Here is a little example with a Gaussian copula and normal and log-normal marginal distributions. I use pairs.panels to illustrate the steps along the way.
I start with standardised multivariate normal random numbers:
library(psych) library(MASS) Sig <- matrix(c(1, -0.7, -.5, -0.7, 1, 0.6, -0.5, 0.6, 1), nrow=3) X <- mvrnorm(1000, mu=rep(0,3), Sigma = Sig, empirical = TRUE) pairs.
The other day I had data that showed the development of many products over time. I grouped the products into categories and visualised the data as line graphs in lattice. But instead of adding an extensive legend to the plot I wanted to add labels to each line’s latest point. How do you do that? It turns out that panel.groups is there to help again.
Here is my solution: R code Session Info R version 3.
For most purposes PDF or other vector graphic formats such as windows metafile and SVG work just fine. However, if I plot lots of points, say 100k, then those files can get quite large and bitmap formats like PNG can be the better option. I just have to be mindful of the resolution.
As an example I create the following plot:
x <- rnorm(100000) plot(x, main="100,000 points", col=adjustcolor("black", alpha=0.2)) Saving the plot as a PDF creates a 5.
Last Tuesday I attended the LondonR user group meeting, where Rich and Andy from Mango argued about the better package for multivariate graphics with R: lattice vs. ggplot2.
As part of their talk they had a little competition in visualising London Underground performance data, see their slides. Both made heavy use of the respective panelling / faceting capabilities. Additionally Rich used the panel.groups argument of xyplot to fine control the content of each panel.
Often I like to reduce the alpha value (level of transparency) of colours to identify patterns of over-plotting when displaying lots of data points with R. So, here is a tiny function that allows me to add an alpha value to a given vector of colours, e.g. a RColorBrewer palette, using col2rgb and rgb, which has an argument for alpha, in combination with the wonderful apply and sapply functions.
Last week I attended a seminar where a talk was given about the economic opportunities in the SAAAME (South-America, Asia, Africa and Middle East) regions. Of course a map was shown with those regions highlighted. The map was not that disimilar to the one below.
library(RColorBrewer) library(rworldmap) data(countryExData) par(mai=c(0,0,0.2,0),xaxs="i",yaxs="i") mapByRegion( countryExData, nameDataColumn="GDP_capita.MRYA", joinCode="ISO3", nameJoinColumn="ISO3V10", regionType="Stern", mapTitle=" ", addLegend=FALSE, FUN="mean", colourPalette=brewer.pal(6, "Blues")) It is a map that most of us in the Northern hemisphere see often.
Lattice plots are a great way of displaying multivariate data in R. Deepayan Sarkar, the author of lattice, has written a fantastic book about Multivariate Data Visualization with R [1]. However, I often have to refer back to the help pages to remind myself how to set and change the legend and how to ensure that the legend will use the same colours as my plot. Thus, I thought I write down an example for future reference.
Michael Bach, who is a professor and vision scientist at the University of Freiburg, maintains a fascinating site about visual illusions. One visual illusion really surprised me: the sigma motion. The sigma motion displays a flickering figure of black and white columns. Actually it is just a chart, as displayed below, with the columns changing backwards and forwards from black to white at a rate of about 30 transitions per second.
Waterfall charts are sometimes quite helpful to illustrate the various moving parts in financial data, particularly when I have positive and negative values like a profit and loss statement (P&L). However, they can be a bit of a pain to produce in Excel. Not so in R, thanks to the waterfall package by James Howard. In combination with the latticeExtra package it is nearly a one-liner to produce a good looking waterfall chart that mimics the look of The Economist: