/baRcodeR

Labeling, tracking, and organizing samples with 2D barcodes

Primary LanguageRGNU General Public License v3.0GPL-3.0

baRcodeR

Status Downloads Codecov test coverage Project Status: Active – The project has reached a stable, usable state and is being actively developed. CRAN checks rOpenSci peer-review

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

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.

Flowchart of major functions

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 4.1.3 (2022-03-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 22000)
## 
## 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_0.1.7 qrcode_0.1.4  
## 
## loaded via a namespace (and not attached):
##  [1] png_0.1-7         assertthat_0.2.1  digest_0.6.29     R.methodsS3_1.8.1
##  [5] magrittr_2.0.2    evaluate_0.15     highr_0.9         rlang_1.0.2      
##  [9] stringi_1.7.6     cli_3.2.0         rstudioapi_0.13   R.oo_1.24.0      
## [13] R.utils_2.11.0    rmarkdown_2.13    tools_4.1.3       stringr_1.4.0    
## [17] xfun_0.30         yaml_2.3.5        fastmap_1.1.0     compiler_4.1.3   
## [21] htmltools_0.5.2   knitr_1.38

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.

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