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Introduction

The juicr package for R contains tools for facilitating the extractions of numerical data from scientific images – like scatter-plots, bar-plots, and other charts/figures found in publications. Below is a description of functionalities and layout.

Updates to this vignette will be posted on our research webpage at USF.

For the source code of juicr see: http://cran.r-project.org/web/packages/juicr/index.html.


Acknowledgements

I thank everyone who watched my YouTube course Hard-boiled Synthesis and reached out to me about using juicr – you gave me the final push to complete this old project I started way back and abandoned in 2017!


How to cite? TBA, but for this beta version maybe:

Lajeunesse, M.J. (2021) Squeezing data from scientific images with the juicr package for R. R package, v. 0.1. CRAN


Installation and Dependencies

juicr has an external dependency that needs to be installed and loaded prior to use in R. This is the EBImage R package (Pau et al. 2010) available only from Bioconductor repository.

To properly install juicr, use the following script in R:

# first load Bioconductor resources needed to install the EBImage package 
# and accept/download all of its dependencies
install.packages("BiocManager"); 
BiocManager::install("EBImage")

# then load juicr
library(juicr)

Finally for Mac OS users, installation is sometimes not straighforward, as the GUI_juicr() requires the Tcl/Tk GUI toolkit to be installed. You can get this toolkit by making sure that the latest X11 application (xQuartz) is installed from here: xquartz.macosforge.org.


Report a bug? Have comments or suggestions?

Please email me any bugs, comments, or suggestions and I’ll try to include them in future releases: . Also try to include juicr in the subject heading of your email. Finally, I’m open to almost anything, but expect a lag before I respond and/or new additions are added.


Video tutorials on Youtube

Image name


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GUI layout and loading images

When running juicr without a file specified, the layout is simple:


main juicr input/ouput bar


Images can be loaded into juicr using the add new image(s) button. Alternatively one or many images (as a vector of file name strings) can be included via console:

# then load juicr
library(juicr)
GUI_juicr("Kam_et_al_2003_Fig2.jpg")
# or many files
GUI_juicr(c("Kam_et_al_2003_Fig2.jpg", "Kortum_and_Acymyan_2013_Fig4.jpg"))
If an image is loaded, the main window will look like this: