rOpenSci: The baRcodeR package

baRcodeR generates labels for more repeatable workflows with biological samples

Installation

You can install the released version of baRcodeR from CRAN with:

install.packages("baRcodeR")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("ropensci/baRcodeR", build_vignettes = T)
# for windows users to build vignettes
# install_github("ropensci/baRcodeR", build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE)

NOTE: Restarting RStudio is necessary for the addin for baRcodeR to appear.

Quick Start

Text identifiers can be created in a sequential or hierarchical pattern.

library(baRcodeR)

## Loading required package: qrcode

## Registered S3 method overwritten by 'R.oo':
##   method        from       
##   throw.default R.methodsS3

example_labels <- uniqID_maker(user = FALSE, string = "Example", level = 1:80)
head(example_labels)

##        label ind_string ind_number
## 1 Example001    Example        001
## 2 Example002    Example        002
## 3 Example003    Example        003
## 4 Example004    Example        004
## 5 Example005    Example        005
## 6 Example006    Example        006

Then the text identifiers can be printed out with a laser printer on sticker sheets.

pdf_file_name <- tempfile()
create_PDF(Labels = example_labels, name = pdf_file_name)

Th particular layout above defaults to ULINE 1.75" * 0.5" labels but other layouts can be specified through parameters in the custom_create_PDF function.

Introduction

baRcodeR is a R package for generating unique identifier strings and printable 2D (QR) barcodes, with the aim of improving repeatability of labelling, tracking and curating data from biological samples. Specifically, users can:

• generate simple ID codes (Ex001, Ex002, Ex003 …),
• generate hierarchical (i.e. nested) ID codes (A01-B01, A01-B02, A02-B01, A02-B02, A03-B01 …),
• generate printable PDF files of paired ID codes and QR barcodes with default spacing for ULINE 1.75" * 0.5" WEATHER RESISTANT LABEL for laser printer; item # S-19297 (uline.ca)
• customize the PDF layout for any type of printable format (e.g, vinyl stickers, waterproof paper)
• generate reproducible code for archival purposes (e.g. in publications or online repositories)
• create CSV files to link unique IDs and sampling hierarchy with downstream data collection workflows. For example, the PyTrackDat pipeline can be used to set up a web-based data collection platform: https://github.com/pytrackdat/pytrackdat

Creating unique, scannable barcodes generally involves two steps:

1. Generate unique ID codes with uniqID_maker() or uniqID_hier_maker()
2. Create a PDF file containing unique ID codes coupled with 2D barcode using create_PDF()

If you already have ID codes saved in a CSV file, the csv can be read into a data.frame() in R. The label column, if it exists will be used as input to generate barcodes. Otherwise, the first column in the data frame will be used.

NOTE: When printing from pdf, ensure that ‘anti-aliasing’ or ‘smoothing’ options are turned OFF, and that you are not using ‘fit to page’ or similar options that will re-scale the output.

Cheat Sheet

A 2-page, quick-reference guide is available via Figshare

Usage with RStudio addin

Please load the vignette “Use Addin”.

library(baRcodeR)
vignette("use-addin")

Usage from the console

Please load the vignette “Using-baRcodeR” for console use.

vignette("Using-baRcodeR")

Contribution

Please note that the ‘baRcodeR’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Please document issues with a description, a minimal reproducible example, and the sessionInfo().

sessionInfo()

## R version 3.6.1 (2019-07-05)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 17763)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252   
## [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
## [5] LC_TIME=English_Canada.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] baRcodeR_0.1.4 qrcode_0.1.1  
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.3        png_0.1-7         digest_0.6.23     R.methodsS3_1.7.1
##  [5] magrittr_1.5      evaluate_0.14     rlang_0.4.1       stringi_1.4.3    
##  [9] rstudioapi_0.10   R.oo_1.22.0       R.utils_2.9.0     rmarkdown_1.17   
## [13] tools_3.6.1       stringr_1.4.0     xfun_0.11         yaml_2.2.0       
## [17] compiler_3.6.1    htmltools_0.4.0   knitr_1.26

See also:

• zintris an R interface to the C zint library. Use zintr if you want to create single barcode images. zintr does not include functions for (i) automating the creation of biologically-relevant, unique ID codes or (ii) customizable layouts for printing multiple barcodes.

• zint is a C library that generates a variety of different barcodes. Just like zintr, zint produces single barcode images.