/baRcodeR

Labeling, tracking, and organizing samples with 2D barcodes

Primary LanguageRGNU General Public License v3.0GPL-3.0

baRcodeR

Status Downloads Travis build status Codecov test coverage Project Status: Active – The project has reached a stable, usable state and is being actively developed. CRAN checks

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.

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 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:

  • zintr is 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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