Posts

This post contains an adapted R script based on prep_n_run_GOplot.pl from Trinity, the denovo transcriptome assembler, for the times R cannot read in the produced EC.* files. prep_n_run_GOplot.pl is used to produce GOplot visualizing differential expression, sorted by GO terms (see http://wencke.github.io/). It uses the DE_analysis.DE_subset and DE.subset.GOseq.enriched files to produce two other files, EC.david. and EC.genelist used in GOplot. In most cases, this script words properly. However, sometimes when the text annotation contains special characters such as , EC.

The sheer variety of geom_* in ggplot2 is overwhelming and astounding, especially with the control over the many aesthetics such as shape and color. For example, the ggplot2 cheat sheet is packed (link). I frequently forget which aes parameters exist for each geom_* and need a quick look at the help pages. Using the information from the cheatsheet, I was able to quickly summarize the aes parameters available for each geom_* (link).

Getting native/introduced status of trees from the USDA PLANTS database using City of Vancouver street trees.

Yihui’s minimal theme for blogdown is wonderful but the Academic theme by G. Cushen provides several benefits, the main one for me being the site is essentially a better-looking electronic CV. blogdown + hugo also makes it easy for me to add images and keep everything organized on a git repository from within RStudio. Unlike many other themes, Academic has several different page types beyong the typical post such as project, and publication.

Announcement of baRcodeR 1.1 and my reason for feature decisions

Bash and R script for extracting SNPs and visualizing SNP distributions from stacks parameter testing

Repost of BIOL 812 tutorial on making an R package. Ends with a function to get references in a data frame from a DOI.

Creating a spatial density map of cherry trees in Vancouver.

Avoid the mishmash of unformatted text in the summary for a post.

This post is for tracking changes to the theme. How to change theme colors: from Leslie Myint This forest green theme uses the dark blue menu bar from the dark theme # Theme metadata name = "Forest" # Is theme light or dark? light = true # Primary primary = "#4caf50" primary_light = "#80e27e" primary_dark = "#087f23" # Menu menu_primary = "#151723" menu_text = "#fff" menu_text_active = "#1b5e20" menu_title = "#fff" # Home sections home_section_odd = "rgb(255, 255, 255)" home_section_even = "rgb(247, 247, 247)" This dark theme is modified from the Academic’s dark theme.