Deciphering Life: One Bit at a Time

Weird Correlation Patterns

If you use kendall-tau on a lot of features, with low numbers of samples, weird things may happen.
R
correlation
analysis
bioinformatics
Using kendall-tau on a lot of features, with lower numbers of samples to calculate the correlation across, may result in very weird looking histograms of the correlation…
Apr 3, 2024
Robert M Flight

 

Installing OpenBLAS for self-compiled R

How to compile, and make sure a self-compiled R uses OpenBLAS, which may be faster than the installed one.
R
profiling
openblas
When you compile R from scratch on Linux, it doesn’t use the system BLAS libraries, it uses one that is compiled itself. This BLAS library may be rather slow. If you want to…
Nov 1, 2023
Robert M Flight

Fast Kendall-tau Correlation with Rcpp

How we created a fast implementation of Kendall-tau using Rcpp
c++
R
packages
Check out our {ICIKendallTau} R package if you want access to a fast version of Kendall-tau correlation in R (Robert M. Flight and Moseley 2022b) with only a few dependencies.
May 29, 2023
Robert M Flight

 

targets and Safe Functions

How to make sure {targets} recognizes changes to a ‘safe’ function?
R
targets
workflow
purrr
If you are using the {targets} workflow manager for your analyses, and also using {purrr::safely} (or others) to control possible errors, do not do the simplest version of…
May 8, 2023
Robert M Flight

 

Blog Posts as Email Newsletters

With the new blog2newsletter, you can have email subscribers to your blog controlled by R thanks to gmailr, googlesheets4, and tidyRSS.
R
newsletters
Want to be able to have people subscribe to your blog via email? Check out the {blog2newsletter} package on GitHub (Flight, n.d.).
Jan 19, 2023
Robert M Flight

Climate Data to Analyze Days by Low Temperatures

Inspired by XKCD to figure out how to get local temperature data and plot it.
xkcd
climate-data
In the past few years I’ve seen a lot of spiral graphs of temperature anomolies, temperature records knit into scarves, among others. But, hats off to Randall Munroe’s XKCD…
Dec 27, 2022
Robert M Flight

Journal Impact Factor Distributions

Discovering that journal impact factor distributions are log-normal.
impact-factor
Journal impact factor distributions seem to be log-normal. If we decide they should be used, then at the very least, they should be log-transformed before doing any…
Dec 25, 2022
Robert M Flight

 

targets and Child Documents

How to make sure that main documents update when a child document is modified in a targets workflow.
random-code-snippets
quarto
rmarkdown
targets
Make sure the child document is a target of the workflow, and that the child document target is loaded in the main.
Dec 22, 2022
Robert M Flight

 

Customizing the Displayed Date in Quarto Pubs

Making the date field more useful in quarto docs and publications.
quarto
R
random-code-snippets
If you want to change how the date is displayed in your {quarto} documents, this is handy.
Dec 8, 2022
Robert M Flight

Measuring Changes in Height Over Time

I have a citizen science project I want to try, that involves individuals measureing their own height daily over a long period of two months. I think I figured out how to do it.
R
development
citizen-science
height
I have a possibly really weird theory, that I’ve not been able to find any literature on. I think that over the course of a full menstrual cycle, that some women’s height…
Dec 7, 2022
Robert M Flight

 

Using Academicons in Your Quarto Blog

If you have trouble getting the academicons in your quarto blog, this might help you too!
random-code-snippets
quarto
Install the academicons extension in your Quarto project, and then use the “text” option.
Dec 3, 2022
Robert M Flight

 

Creating an Analysis With a targets Workflow

How I work through an -omics analysis using the targets package.
analysis
development
mass-spectrometry
targets
Setting up an analysis workflow using {targets} can be a little confusing without worked examples. This is my attempt to provide such an example.
Sep 27, 2022
Robert M Flight

 

Compiling Against Python.h

How to make sure that cython can find python.h when using a self compiled python.
python
cython
random-code-snippets
Sometimes, the installed version of Python on your linux system isn’t what you need, and you can’t easily install a newer version system-wide. Of course, you can download…
Jun 22, 2022
Robert M Flight

Project Consultation Template

What our labs project consult template looks like.
research
A little while ago, I was tweeting about the joy of collaborating with people who haven’t included you in their experimental design. One of the tweets was this:
Feb 8, 2022
Robert M Flight

 

Heatmap Colormaps!

Examples of good colormaps to use for heatmaps, both divergent and incremental.
colormaps
visualization
heatmap
random-code-snippets
Nine times out of ten, you probably need just one of the {viridis} colormaps for values that are increasing in one direction. For example, correlation values that are all…
Jan 31, 2022
Robert M Flight

Recreating Correlation Values from Another Manuscript

Documenting my journey trying to recreate some correlations calculated in another manuscript.
reproducibility
correlation
I’ve been working on a manuscript for our newish correlation method, information-content-informed Kendall-tau (ICI-Kendalltau, package currently at (Flight and Moseley 2021))…
Jan 15, 2022
Robert M Flight

 

Cairo and XQuartz in Mac GitHub Actions

Including cairo and xquartz in MacOS github actions
random-code-snippets
cairo
xquartz
development
github
R
I’ve been using GitHub actions to check and test some of my R packages on multiple architectures, which is nice because I work primarily on Linux.
Jan 6, 2022
Robert M Flight

 

Dplyr in Packages and Global Variables

How to include dplyr in a package, and avoid warnings around global variables.
random-code-snippets
packages
dplyr
rlang
R
development
I was recently cleaning up a development package so it would actually pass checks so it could be hosted on our labs new r-universe (“The ’Moseleybioinformaticslab’ Universe,”…
Jan 6, 2022
Robert M Flight

 

Pie Charts in RCy3

How to represent nodes as pie charts using Cytoscape and RCy3
random-code-snippets
rcy3
cytoscape
R
I have a package, {categoryCompare2} (Flight 2022) that I’ve been working on for a while, and recently wanted to make available on our labs r-universe (“The…
Jan 6, 2022
Robert M Flight

 

Reusing ggplot2 Colors

When you want to reuse ggplot2 default colors across plots.
random-code-snippets
ggplot2
visualization
If you are using {ggplot2} a lot in your code, and don’t want to bother with a custom color scheme (I mean, there are lots of good options), but you are also using…
Dec 21, 2021
Robert M Flight

 

Migrating Self-Hosted GitLab Projects to GitHub

We wanted to migrate from self-hosted GitLab projects to GitHub repos. Here is some background on how we accomplished that.
version-control
github
gitlab
Six years ago, we didn’t really look into what the free academic version of GitHub teams provided for private repositories, and instead decided that we should have a…
Nov 25, 2021
Robert M Flight

Zooming GGraph Plots

Some code demonstrating how to zoom into portions of a ggraph.
graphing
ggraph
visualization
random-code-snippets
I was recently working with a largish graph that I am using the ggraph package, and I needed to zoom into a sub-region of the graph.
Nov 11, 2021
Robert M Flight

 

R CMD Check and Non-PDF Vignettes

R CMD Check complaining about missing files? Here was my solution.
packages
random-code-snippets
If you’ve written an R package that you want hosted by CRAN (or even if not hosted), then you generally want to run the infamous R CMD check on your package.
Oct 27, 2021
Robert M Flight

My Vacation in Barometric Pressure

What can we see from my phone’s barometric pressure readings?
graphing
maps
visualization
I recently took a proper vacation, that involved driving from Lexington, KY, USA to Digby, NS, Canada and all points in between. I also have an app, Barometer Reborn, on my…
Sep 20, 2021
Robert M Flight

 

Random Forest Classification Using Parsnip

How to make sure you get a classification fit and not a probability fit from a random forest model using the tidymodels framework.
parsnip
tidymodels
machine-learning
random-forest
random-code-snippets
I’ve been working on a “machine learning” project, and in the process I’ve been learning to use the tidymodels framework (“Tidymodels” 2021), which helps save you from…
Aug 30, 2021
Robert M Flight
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