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baRcodeR generates labels for more repeatable workflows with biologicalsamples

You can install the released version of baRcodeR fromCRAN with:

install.packages("baRcodeR")

And the development version fromGitHub 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 toappear.

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 onsticker 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 butother layouts can be specified through parameters in thecustom_create_PDF function.

baRcodeR is a R package for generating unique identifier strings andprintable 2D (QR) barcodes, with the aim of improving repeatability oflabelling, 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 withdefault spacing for ULINE 1.75” * 0.5” WEATHER RESISTANT LABEL forlaser 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. inpublications or online repositories)
• create CSV files to link unique IDs and sampling hierarchy withdownstream data collection workflows. For example, the PyTrackDatpipeline 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 withuniqID_maker() oruniqID_hier_maker()
2. Create a PDF file containing unique ID codes coupled with 2D barcodeusingcreate_PDF()

If you already have ID codes saved in a CSV file, the csv can be readinto adata.frame() in R. Thelabel column, if it exists will beused as input to generate barcodes. Otherwise, the first column in thedata 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 topage’ or similar options that will re-scale the output.

A 2-page, quick-reference guide is available viaFigshare

Please load the vignette “Use Addin”.

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

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

vignette("Using-baRcodeR")

Please note that the ‘baRcodeR’ project is released with aContributorCode ofConduct.By contributing to this project, you agree to abide by its terms.

Please document issues with a description, a minimal reproducibleexample, and thesessionInfo().

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

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

• zint is a C library that generates a varietyof different barcodes. Just like zintr, zint produces single barcodeimages.