Archive for June, 2015

MongoDB with D3.js

22 Jun 2015

I consider interactive data visualization to be the critical tool for exploration of high-dimensional data.

That’s led me to spend a good amount of time in the last few years learning some new skills (D3 and CoffeeScript) and developing some new tools, particularly the R package R/qtlcharts, which provides interactive versions of the many data visualizations in R/qtl, my long-in-development R package for mapping genetic loci (called quantitative trait loci, QTL) that underlie complex trait variation in experimental organisms.

R/qtlcharts is rough in spots, and while it works well for moderate-sized data sets, it can’t well handle truly large-scale data, as it just dumps all of the data into the file viewed by a web browser.

For large-scale data, one needs to dynamically load slices of the data based on user interactions. It seems best to have a formal database behind the scenes. But I think I’m not unusual, among statisticians, in having almost no experience working with databases. My collaborators tend to keep things in Excel. Even for quite large problems, I keep things in flat files.

So, I’ve been trying to come to understand the whole database business, and how I might use one for larger-scale data visualizations. I think I’ve finally made that last little conceptual step, where I can see what I need to do. I made a small illustration in my d3examples repository on GitHub.


Randomized Hobbit

22 Jun 2015

@wrathematics pointed me to his ngram R package for constructing and simulating from n-grams from text.

I’d recently grabbed the text of the hobbit, and so I applied it to that text, with amusing results.

Here’s the code I used to grab the text.

stem <- ""
hobbit <- NULL
for(i in 1:74) {
    if(i==1) {
        url <- paste0(stem, ".html")
    } else {
        url <- paste0(stem, "_", i, ".html")

    x <- htmlTreeParse(url, useInternalNodes=TRUE)
    xx <- xpathApply(x, "//p", xmlValue)
    hobbit <- c(hobbit, gsub("\r", "", xx[-length(xx)]))

Then calculate the ngrams with n=2.

ng2 <- ngram(hobbit, n=2)

Simulate some number of words with babble(). If you use the seed argument, you can get the result reproducibly.

babble(ng2, 48, seed=53482175)

into trees, and then bore to the Mountain to go through?” groaned the hobbit. “Well, are you doing, And where are you doing, And where are you?” it squeaked, as it was no answer. They were surly and angry and puzzled at finding them here in their holes

Update: @wrathematics suggested that I mix two texts, so here’s a bit from the Hobbit in the Hat (The Hobbit with 59× Cat in the Hat — up-sampled to match lengths.) But there’s maybe not enough overlap between the two texts to get much of a mixture.

“I am Gandalf,” said the fish. This is no way at all!

already off his horse and among the goblin and the dragon, who had remained behind to guard the door. “Something is outside!” Bilbo’s heart jumped into his boat on to sharp rocks below; but there was a good game, Said our fish No! No! Those Things should not fly.