Random Code Snippets

Customizing the Displayed Date in Quarto Pubs

Making the date field more useful in quarto docs and publications.

If you want to change how the date is displayed in your {quarto} documents, this is handy.
Dec 8, 2022
Robert M Flight

Heatmap Colormaps!

Examples of good colormaps to use for heatmaps, both divergent and incremental.

Nine times out of ten, you probably need just one of the {viridis} colormaps for values that are increasing in one direction. For…
Jan 31, 2022
Robert M Flight

Cairo and XQuartz in Mac GitHub Actions

Including cairo and xquartz in MacOS github actions

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

Pie Charts in RCy3

How to represent nodes as pie charts using Cytoscape and RCy3

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

Dplyr in Packages and Global Variables

How to include dplyr in a package, and avoid warnings around global variables.

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,” n.…
Jan 6, 2022
Robert M Flight

Reusing ggplot2 Colors

When you want to reuse ggplot2 default colors across plots.

If you are using {ggplot2} a lot in your…
Dec 21, 2021
Robert M Flight

Zooming GGraph Plots

Some code demonstrating how to zoom into portions of a ggraph.

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.

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

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.

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 leaking information from testing to training data, as well as creating…
Aug 30, 2021
Robert M Flight

Coloring Dendrogram Edges with ggraph

Here is how I got edges colored in a dendrogram with ggraph. Use “node.” in front of the node data column you want.

I wanted to…
Aug 3, 2021
Robert M Flight

Keeping Figures in an Rmd – Word Document

How to make your rmarkdown to word conversion also generate a directory of figures.

I’ve been working with a lot of collaborators who expect Word documents lately. I…
Jul 22, 2021
Robert M Flight

Highlighting a Row of A ComplexHeatmap

A simple way to highlight or bring attention to a row or column in a ComplexHeatmap.

The ComplexHeatmap Bioconductor package (Gu, Eils, and Schlesner 2016; Gu 2021a, 2021b) has become my goto for visualizing sample-sample correlation heatmaps, which I use a lot. Recently, I…
Mar 26, 2021
Robert M Flight

Random Code Snippets

Introducing random-code-snippets.

I’ve been organizing a bunch of random code that I find myself re-using time and time again in a Github Repo (Flight, n.d.). But the repo is not very searchable unless you are the one who…
Mar 5, 2021
Robert M Flight

Custom Deployment Script

I don’t want to use Netlify for hosting, so I came up with this simple script to deploy my blog.

Use a short bash script to do deployment from your own computer directly to your *.github.io domain.
Dec 27, 2017
Robert M Flight

Package Version Increment Pre- and Post-Commit Hooks

Two git commit hooks for incrementing the package version as part of commits.

If you just want the hook scripts, check this gist. If you want to know some of the motivation behind writing them, and about the internals, then read on.
Feb 7, 2014
Robert M Flight

Creating Custom CDFs for Affymetrix Chips in Bioconductor

Examples of messing with Affymetrix CDF data in Bioconductor.

For those who don’t know, CDF files are chip definition format files…
Jul 13, 2012
Robert M Flight
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