Problem Setup In recent question on LinkedIn’s R user group, a user asked “How to normalize by the row sums of the variable?”. Now first, we must define what we mean by “normalize” a matrix/data.frame. One way to standardize/normalize a row is to subtract by the ...

Recently, Jeff Leek at Simply Statistics discussed why he does not use ggplot2. He notes “The bottom line is for production graphics, any system requires work.” and describes a default plot that needs some work: To break down what is going on, here is what R interprets (more or less): ...

In my post of recommendations for first-year students, I discussed some tips and viewpoints to help the practical, pragmatic aspects about being a first year student. In this post, I'd like to discuss the common misconceptions/viewpoints that are destructive to new students. The Dunning-Kruger effect I know something, so ...

In a previous post, I described how you can interactively explore a 3D nifti object in R. I used the manipulate package, but the overall results were sluggish and not really usable. I was introduced to a a good neuroimaging viewer called Mango, by a friend or two and use ...

I recently had an email for a colleague asking me to make a figure like this in ggplot2 or trellis in R: As I know more about how to do things in ggplot2, I chose to use that package (if it wasn't obvious from the plot or other posts). Starting ...

Manipulate Package The manipulate from RStudio allows you to create simple Tcl/Tk operators for interactive visualization. I will use it for a simple slider to view different slices of an image. fslr package I'm calling the fslr package because I know that if you have it installed, you will ...

Goals and Overall Approach We will use multiple packages and pieces of software for white matter (and gray matter/cerebro spinal fluid (CSF)) segmentation. The overall approach will be, with the required packages in parentheses: N4 Inhomogeneity Bias-Field Correction (extrantsr and ANTsR) Brain extraction using BET and additional tools (extrantsr ...

It’s almost ENAR 2015! The final program is out with all the sessions. The last conference I went to, the International Stroke Conference, had a program planner hosted by abstracts online. Although there are parts of this system I would like to change, I believe it is helpful for looking ...

This is the first post I’ve written in a while. I have been somewhat radio silent on social media, but I’m jumping back in. Now, I work with brain images, which can have millions of elements (referred to as voxels). Many of these elements are zero (for background). ...

Recently, my colleague and fellow blogger Alyssa Frazee accepted a job at Stripe. All of us at JHU Biostat are happy for her, yet sad to see her go. While perusing Stripe’s website, I found the About page, where each employee has a photo of themselves. I’ve been ...

In my last post, I gave an introduction of the ROCR package and how to use it for ROC analysis. In the ROCR reference manual, it states “new performance measures can be added using a standard interface”, but I have not found that to be so. I may have missed ...

I've been doing some classification with logistic regression in brain imaging recently. I have been using the ROCR package, which is helpful at estimating performance measures and plotting these measures over a range of cutoffs. The prediction and performance functions are the workhorses of most of the analyses in ROCR ...

In my last post I described some of my commonly done ggplot2 graphs. It seems as though some people are interested in these, so I was going to follow this up with other plots I make frequently. Scatterplot colored by continuous variable The setup of the data for the scatterplots ...