Blog Archives

Functions for plotting and getting Greek in labels

October 8, 2012
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Functions for plotting and getting Greek in labels

The problem: We often want to plot data and assign plot attributes based on characteristics of the data. For example, if we have a group of students with the following IQs, we might want to indicate who is an outlier in the statistical sense. I like...

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Calculating distances (across matrices)

October 5, 2012
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Calculating distances (across matrices)

This Gist is mostly for my future self, as a reminder of how to find distances between each row in two different matrices. To create a distance matrix from a single matrix, the function dist(), from the stats package is sufficient. There are times, ho...

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Log odds ratios and an indicator matrix from categorical data

October 4, 2012
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Log odds ratios and an indicator matrix from categorical data

A long title, but there are a couple of handy things in this Gist. The first, and more obscure, is the conversion of a data.frame of categorical variables into a matrix of dummy/binary/indicator variables, one for each category of each original variab...

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Transforming a color scale

October 3, 2012
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Transforming a color scale

In developing plots, I often use color (or “colour” in ggplot2 parlance) to reflect values of a third, non-X/Y, variable. Depending on the distribution of this Z variable, however, the effective color range can be narrow, making it difficul...

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A replacement for theme_blank()

October 2, 2012
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A replacement for theme_blank()

ggplot2 has just hit 0.9.2, and with the change comes a new theme system. Previous versions of ggplot2 offered a theme_blank(), which was a stripped-down, essentially blank plotting canvas, but it is now deprecated. github user jrnold has produced a s...

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Making random, equally-sized partitions

October 1, 2012
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Making random, equally-sized partitions

Sometimes, as with cross-validation, one needs to generate k partitions, each with an equal number of observations. There are probably an infinite number of ways this could be done in R, but the Gist below illustrates one way to do it in four lines, w...

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Optimal seriation for your matrices

September 28, 2012
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Optimal seriation for your matrices

In our previous post, we used a quick-and-dirty method for ordering the axes on our heatmap. It has been pointed out to me that There is a Package for That (which is my nominee for a new slogan for R — not that it needs a slogan). seriation offe...

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Simplest possible heatmap with ggplot2

September 27, 2012
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Simplest possible heatmap with ggplot2

Featuring the lovely “spectral” palette from Colorbrewer. This really just serves as a reminder of how to do four things I frequently want to do: Make a heatmap of some kind of matrix, often a square correlation matrix Reorder a factor vari...

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Modifying select off-diagonal items in a matrix

September 25, 2012
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This is something I have had the occasion to do, and never remember how, so this is legitimately a reminder to my future self of how to do things with off-diagonal elements of a matrix. Select rows and columns are easy: mat or mat, for...

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Visually-weighted regression plots, with Zelig

September 25, 2012
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Visually-weighted regression plots, with Zelig

As a follow-up to yesterday’s post on producing visually-weighted regression plots, here is some code which illustrates the production of similar plots, but using Zelig’s convenient modeling and simulation functions. This code was produced...

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