Category Archives: general

Turning off Auctex fontification so that columns can align

I love Emacs. I use it for everything, and particularly love it for doing tables in LaTeX because I can easily align everything so that it looks sensible, and rectangle mode makes it easy to move columns around if desired.

That being said, Auctex defaults do some fontification to math-mode super- and subscripts, which cause the horizontal alignments of characters to be off (essentially it is no longer a fixed-width font). To turn this off, do:

M-x customize-variable font-latex-fontify-script

Beauty!

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Anti-aliasing and “image” plots

Introduction

Frequently I make plots using the oce1 function imagep(), which at it’s core using the R-base function image(). R has several different graphics devices to choose from, and as each of them have different schemes for tasks such as anti-aliasing they can produce different results depending on the type of plot being created, and the type of file it gets written to. This can be especially apparent when using the filledContour type of plot. Frequently, I find that the default devices for making such plots in R produces undesirable artifacts, such as white lines in an image plot. The example below illustrates this effect using the adp data set:

library(oce)
data(adp)
imagep(adp[["v"]][, , 1], filledContour = TRUE)

plot of chunk plotWithLines

In this post I’ll explore some options for making plots without such artifacts.

PDF devices

It is common for anti-alias effects like the white lines shown above to show up in figures created using the pdf() device. As PDF is essentially a vector graphics format, there is nothing to be done in R to correct the problem. Typically the anti-aliasing is handled by the PDF viewer, and is therefore not native to the file. It is often possible to disable anti-aliasing in many of the most popular viewers (e.g. I use Skim and Preview on OSX), but this has the unfortunate side effect of removing anti-aliasing from all aspects of the figure, including the fonts and axes labels, etc.

For this reason, when producing image plots, I almost always default to using a PNG device instead of a PDF. PNG works perfectly well with pdflatex, and has no artifacts due to image compression (such as in JPGs). The only issue remaining is how to ensure that the image plot itself does not suffer from anti-aliasing effects, while retaining the smoothing of fonts, lines, and points to make a beautiful plot.

PNG devices

For PNG devices, there are several options for the “type” of device, each of which will produce slightly different output. From the help page for png(), the arguments are:

png(filename = "Rplot%03d.png",
width = 480, height = 480, units = "px", pointsize = 12,
bg = "white", res = NA, ...,
type = c("cairo", "cairo-png", "Xlib", "quartz"), antialias)

where the type argument is described as:

type: character string, one of ‘"Xlib"’ or ‘"quartz"’ (some OS X
builds) or ‘"cairo"’. The latter will only be available if
the system was compiled with support for cairo - otherwise
‘"Xlib"’ will be used. The default is set by
‘getOption("bitmapType")’ - the ‘out of the box’ default is
‘"quartz"’ or ‘"cairo"’ where available, otherwise ‘"Xlib"’.

Let’s try some examples of each of the type options to see the difference.

types <- c("cairo", "cairo-png", "Xlib", "quartz")
for (itype in seq_along(types)) {
png(paste("typeExample-", types[itype], ".png", sep = ""), type = types[itype],
width = 300, height = 300)
imagep(adp[["v"]][, , 1], filledContour = TRUE, main = types[itype])
dev.off()
}

each of which produces the following:

cairo cairo cairo cairo

Note that it is the default quartz type that produces the issues through anti-aliasing. This can be turned off by specifying antialias='none' (see the description of the antialias are from ?png for more details):

png("quartzNoAntialias.png", type = "quartz", antialias = "none")
imagep(adp[["v"]][, , 1], filledContour = TRUE, main = "quartz with antialias=none")
dev.off()
## pdf
## 2

quartzNoAntialias

This “fixes” the problem for the image plot, but leaves the fonts and axis lines un-antialiased.

Summary

Based on the above, the best option for producing image-style plots without antialiasiaing artifacts is to use the type='cairo' option for the png device (note that by default Cairo devices use the Helvetica font family, whereas Quartz devices use Arial).

png("cairoDevice.png", type = "cairo", antialias = "none", family = "Arial")
imagep(adp[["v"]][, , 1], filledContour = TRUE, main = "A Cairo device png")
dev.off()
## pdf
## 2

cairoDevice


  1. For hints on installing the oce package check out the blog post here 

Switching from Matlab to R: Part 1

Introduction

I was thinking recently about how best to help someone transitioning
from Matlab(TM) to R, and did my best to recall what sorts of things I
struggled with when I made the switch. Though I resisted for quite a
while, when I finally committed to making the change I recall that it
mostly happened in a matter of weeks. It helped that my thesis
supervisor exclusively used R, and we were working on code for a paper
together at the time, but in the end I found that the switch was
easier than I had anticipated.

Tips

  1. Don’t be afraid of the assign &lt;- operator. It means exactly the
    same thing as you would use = in matlab, as in
a <- 1:10 # in matlab a=1:10;

except that it make more logical sense.

The only place you should use = is in logical comparisons like a ==
b
(as in matlab), or for specifying argument values in a function
(see number 5).

  1. Vectors are truly 1 dimensional. This is different from matlab in
    the way that you could not add together an Nx1 and a 1xN vector. In
    R it would be just two vectors of length N. The transpose in R is
    by doing t(), and the transpose of a vector (or class numeric)
    is the same as the original.

  2. Array indices use square brackets, like

a[1:5] <- 2 # assign the value 2 to the first 5 indices of a

This is one of the things that drove me crazy about matlab, that it
used () for indices as well as function arguments. It makes mixed
array indexing and function calls very confusing to look at and
interpret.

  1. By default arithmetic operations are done element-wise. If you have
    two MxN matrices (say A and B), and you do C &lt;- A*B, every
    element in C is the product of the corresponding elements in A and
    B. No need to do the .* stuff as in matlab. To get matrix
    multiplication, you use the %*% operator.

  2. Function arguments are named, so the order isn’t super
    important. If you don’t name them, then you have to give them in
    the order they appear (do ?function to see the help page). For
    example if a function took arguments like:

foo <- function(a, b, c, type, bar) {
# function code here
}

You could call it with something like:

junk <- foo(1, 2, bar = "whatever")

where a and b are given the values of 1 and 2, and c and type
are left unspecified. This would be equivalent:

junk <- foo(a = 1, b = 2, bar = "whatever")

You could also do:

junk <- foo(bar = "whatever", a = 1, b = 2)
  1. No semicolons needed (except where you’d like to have more than one
    operation per line, like a &lt;- 1; b &lt;- 2

  2. In R, the equivalent to a matlab structure is called a
    “list”. Instead of separating the levels with a ., it is
    generally done with a $. So the structure of a list could be
    something like:

a <- junk$stuff$whatever

Use the str() command to look at the structure of a list object.

  1. Most functions that return more than just a single value will
    return in a list. Unlike matlab there isn’t a simple way returning
    separate values to separate variables, like [a, b] =
    foo('bar')
    . For example, using the histogram function:
a <- rnorm(1000)
h <- hist(a)

plot of chunk unnamed-chunk-8

str(h)
## List of 6
## $ breaks : num [1:16] -4 -3.5 -3 -2.5 -2 -1.5 -1 -0.5 0 0.5 ...
## $ counts : int [1:15] 1 1 3 24 47 80 147 186 206 134 ...
## $ density : num [1:15] 0.002 0.002 0.006 0.048 0.094 0.16 0.294 0.372 0.412 0.268 ...
## $ mids : num [1:15] -3.75 -3.25 -2.75 -2.25 -1.75 -1.25 -0.75 -0.25 0.25 0.75 ...
## $ xname : chr "a"
## $ equidist: logi TRUE
## - attr(*, "class")= chr "histogram"

If I wanted to extract something from that I could use

b <- h$breaks

If you really only want one thing out of the list, you could do
something like

b <- hist(a, plot = FALSE)$breaks
  1. You can use .‘s in variable and function names, but I don’t
    recommend you do. Often a function with a . in it means that it
    applies a “generic” operation to a specific class. For example, the
    plot() function is a straightforward way of plotting data, much
    like in matlab. However, there exist lots of variants of plot for
    different classes, which are usually specified as
    plot.class(). E.g. for the histogram object I created above, if I
    want to plot it, I can just do
h2 <- hist(a, plot = FALSE, breaks = 100)
plot(h2, main = "A plot with more breaks")

plot of chunk unnamed-chunk-11

and it will plot it as a histogram, using the generic function
plot.histogram(), as well as accept the arguments appropriate to
that generic function.

Thoughts on topics for future editions of matlab2R

  • plotting, including:

  • points, lines, styles, etc

  • “image”-style plots, contours, filled contours, colormaps, etc
  • POSIX times vs Matlab datenum

  • … suggestions in comments?

Finding system files with Spotlight on OSX

By default spotlight won’t search through system files (e.g. anything that lives in ~/Library/), which gave me a bit of a headache today when I was looking for where I had put an emacs mode file that I was initializing in my Preferences.el in Aquamacs.

The trick is to enable “System files” in the “Kind” menu in the Finder spotlight. To do this add a search rule, click on the “Kind” menu, choose “Other” and select “System files” in the list. Wham!

From lifehacker.

Using Rmarkdown with knitr to compose WordPress posts

What I’d like to be able to do is use knitr on an R markdown (i.e. .Rmd) document so include text, code, code output, and images to make a nice looking WordPress post that I can compose and edit locally. And advantage to this is that I can use whatever editor I want for doing the composing (like Aquamacs), and that everything is contained in a single source document.

Workflow

I think the flow will be something like:

  1. Create the post in an .Rmd file locally in emacs.

  2. Use knitr with my local version of R to process the Rmd into either a proper md (Markdown) or an HTML that I can just upload (NOTE: the HTML option doesn’t really seem to work … will maybe need to look into this some more).

  3. Upload (or copy/paste) the md or HTML source into WordPress. The big question is what will happen with generated images, etc. With Markdown, I think the images are created in a directory that is dynamically linked to, but for the HTML there is maybe some way that images are embedded (it appears the embedding isn’t compatible with copying and pasting the HTML source produced by knitr — I guess the images will have to be uploaded manually).

Some code

Here is an example:

x <- seq(1, 1000)
y <- rnorm(length(x))
plot(x, y)

plot of chunk unnamed-chunk-1

Post script

Copying and pasting the .md source produced by knitr works pretty well, though the image links will be broken. To fix this, each image produced by knitr needs to be added to the media library, and then inserted into the post to get the proper path. E.g. for the test figure above, the path is https://codedocean.files.wordpress.com/2014/01/unnamed-chunk-1.png. The linking to the image can still be done in a “markdown” way by using something like:

![plot of chunk unnamed-chunk-1](https://codedocean.files.wordpress.com/2014/01/unnamed-chunk-1.png)