Blog Archives

baRcodeR 0.1.2 release – new linear barcodes

January 9, 2019
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baRcodeR 0.1.2 release – new linear barcodes

baRcodeR 0.1.2 is released on CRAN today! Download and install by install.packages("baRcodeR") Example linear barcode The major feature of this release is the ability to print linear (a.k.a normal) barcodes through specifying type = "linear" in create_PDF() rather than type = "matrix" which prints the usual QR code. The github repository is at yihanwu/baRcodeR. Minor notes on the implementation of these linear barcodes The linear barcodes...

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Icon making with ggplot2 and magick

January 2, 2019
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Icon making with ggplot2 and magick

Icon noun A person or thing regarded as a representative symbol or as worthy of veneration. A symbol or graphic representation on a screen of a program, option, or window. from Oxford English Dictionaries Fontawesome and the noun project along with other icon provides produce and distribute beautiful icons for free use. But sometimes, I would like to alter or create my own tiny...

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Blogdown – shortcode for radix-like Bibtex

December 20, 2018
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In the spirit of trying out new things in Hugo since my last post on modifying the RSS feed for this website, I attempted to implement the new citation feature from the new radix package by RStudio. Essentially, I tried using a custom hugo shortcode to replicate the text and BibTex citation at the bottom of the page when rendered...

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RStudio Pandoc – HTML To Markdown

December 14, 2018
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The knitr and rmarkdown packages are used in conjunction with pandoc to convert R code and figures to a variety of formats including PDF, and word. Here, I’m exploring how to convert HTML back to markdown format. This post came about when I was searching how to convert XML to markdown, which I still haven’t found an easy way...

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Rrrrs in R – Letter frequency in R package names

December 6, 2018
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Rrrrs in R – Letter frequency in R package names

R package authors sometimes like to add the letter “r” to package names (for example, the tidyverse packages). baRcodeR also has an extra “r” at the end as well. I thought I could use some available data see if the letter frequency changes compared to the English language average. I used two data sets. The first is the percentage frequency...

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Using taxa and metacoder to explore taxonomy of Vancouver’s trees

November 29, 2018
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Using taxa and metacoder to explore taxonomy of Vancouver’s trees

From the last post, Vancouver has several common genus in its collection, such as Prunus and Acer. So rather than analyzing the diversity of Vancouver tree species on a species level, we could, with the help of some R packages, visualize the variety of taxonomic groups. First, we format the Vancouver tree dataset similar to before to get the proper...

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Vancouver Trees – Vizualizing biodiversity, native and introduced trees

November 22, 2018
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Vancouver Trees – Vizualizing biodiversity, native and introduced trees

Following from the past post, this post is focused on visualizing diversity through the package vegan and also maps showing the presence of native/introduced trees. The most important code in this post is manipulating Spatial*DataFrames. The same files will be read in, including the native/introduced status downloaded from USDA PLANTS. library(rgdal) library(sp) library(raster) library(dplyr) library(httr) library(rvest) library(purrr) library(tidyr) # read in trees df trees_df

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R Script prep for GOplot from Trinity

November 19, 2018
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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...

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Vancouver Trees – Getting Native/Introduced status from USDA

November 16, 2018
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Motivation: I converted a KML shape file into a data frame in my previous post on cherry trees in Vancouver but I figured I should learn to actually work with shape files. I thought an easy figure to make was to show which parts of Vancouver had introduced trees and native trees but it turned out harder than I...

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Mapping ggplot geoms and aesthetic parameters

November 16, 2018
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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...

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