Package 'juicr'

Title: Automated and Manual Extraction of Numerical Data from Scientific Images
Description: Provides a GUI interface for automating data extraction from multiple images containing scatter and bar plots, semi-automated tools to tinker with extraction attempts, and a fully-loaded point-and-click manual extractor with image zoom, calibrator, and classifier. Also provides detailed and R-independent extraction reports as fully-embedded .html records.
Authors: Marc J. Lajeunesse [aut, cre]
Maintainer: Marc J. Lajeunesse <[email protected]>
License: GPL (>= 2)
Version: 0.2
Built: 2025-02-03 03:54:25 UTC
Source: https://github.com/mjlajeunesse/juicr

Help Index

Automated, semi-automated, and manual extraction of numerical data from scientific images, plot, charts, and figures

Description

juicr is a GUI interface for automating data extraction from multiple images containing scatter and bar plots, semi-automated tools to tinker with extraction attempts, and a fully-loaded point-and-click manual extractor with image zoom, calibrator, and classifier. Also provides detailed and R-independent extraction reports as fully-embedded .html records. More information about juicr can be found at http://lajeunesse.myweb.usf.edu/.

Details

What to cite?

Lajeunesse, M.J. (2021) Automated, semi-automated, and manual extraction of numerical data from scientific images, plot, charts, and figures. R package, v.0.1

Installation and Dependencies.

juicr has one external dependency that need to be installed and loaded prior to use in R. This is the EBImage R package (Pau et al. 2010) available only from the Bioconductor repository: https://www.bioconductor.org/.

To properly install juicr, start with the following R script that loads the Bioconductor resources needed to install the EBImage (also accept all of its dependencies):

install.packages("BiocManager");
BiocManager::install("EBImage"))
library(metagear)

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 the latest X11 application (xQuartz) is installed from here: https://www.xquartz.org/.

Author(s)

Marc J. Lajeunesse (University of South Florida, Tampa USA)

References

Pau, G., Fuchs, F., Sklyar, O., Boutros, M. and Huber, W. (2010) EBImage: an R package for image processing with applications to cellular phenotypes. Bioinformatics 26: 979-981.

Reads a *_juicr.html report and retrieves data extractions and history.

Description

Reads a juicr generated report of image extractions contained within the .html file.

Usage

file_getJuicr_Extractions(aFileName = file.choose(), quiet = FALSE)

Arguments

aFileName

The file name and location of a *_juicr.html report. Prompts for file name if none is explicitly called. Must be .html format.
quiet

When "TRUE", does not display all extraction tables.

Value

A list of tables including all extractions, coordinates, image file names, and juicr GUI parameters.

See Also

file_getJuicr_Images

Examples

## Not run: 

theExtraction <- file_getJuicr_Extractions("pretend_image_juicr.html")
print(theExtraction$points)


## End(Not run)

Reads a *_juicr.html report and extracts images into working directory.

Description

Reads a juicr generated report of image extractions contained within the .html file, and saves all images (e.g., original, standardized, and standardized with painted extractions).

Usage

file_getJuicr_Images(aFileName = file.choose(), quiet = FALSE)

Arguments

aFileName

The file name and location of a *_juicr.html report. Prompts for file name if none is explicitly called. Must be .html format.
quiet

When "TRUE", does not display the file names of all images extracted and saved to the working directory.

Value

A vector of file names of each image extracted from the .html file.

See Also

file_getJuicr_Extractions

Examples

## Not run: 

file_getJuicr_Images("pretend_image_juicr.html")


## End(Not run)

A GUI screener to quickly code candidate studies for inclusion/exclusion into a systematic review or meta-analysis.

Description

A GUI screener to help scan and evaluate the title and abstract of studies to be included in a systematic review or meta-analysis. A description of GUI options and layout is found here: http://lajeunesse.myweb.usf.edu/juicr/juicr_basic_vignette_v0.1.html.

Usage

GUI_juicr(
  theFigureFile = "",
  theJuicrFile = "",
  standardizeTheImage = TRUE,
  standardSize = 1000,
  figureWindowSize = c(800, 600),
  pointSize = 6,
  animateDelay = TRUE,
  groupNames = c("orangeGrp", "berryGrp", "cherryGrp", "plumGrp", "kiwiGrp",
    "bananaGrp", "grapeGrp", "pruneGrp"),
  groupColors = c("dark orange", "turquoise3", "tomato3", "orchid", "yellow green",
    "goldenrod2", "plum4", "saddle brown")
)

Arguments

theFigureFile

An optional file name and location of a .jpg, .png, or .tiff file containing the scientific image/plot/chart/figure to pre-load in the GUI. Within the GUI there is also a button to select the image file. Images in other formats should be converted to .png prior to using juicr.
theJuicrFile

An optional file name and location of a *_juicr.html report containing extractions and images from a previous juicr session to pre-load into the GUI. Within the GUI there is also a button to select an .html file.
standardizeTheImage

When "TRUE", all large images are standardized to a common size with a width specified by "standardSize". When "FALSE", the image is unaltered in size.
standardSize

The common width in pixels for standardizing large images; default is a width of 1000 pixels.
figureWindowSize

Specifies the window size containing the image. By default, this image-viewer window will be 800 (width) by 600 (height) pixels, larger images will be scrollable to fit this window.
pointSize

Changes the default size of a clickable data-point on the image. Size is the radius in pixels (default is 6).
animateDelay

When "TRUE", creates a very small pause when plotting individual automated extractions – giving an animated effect.
groupNames

A vector of the default eight names specifying the labels of each group. Default labels are fruit themed. Can be any size, but GUI will only print first 9 characters.
groupColors

A vector of the default eight color names specifying the coloring of each group. Are in color-names format, but can also be HEX.

Value

A console message of where saved .csv or *_juicr.html files are located.

Note

Installation and troubleshooting

For Mac OS users, installation is sometimes not straighforward as this GUI requires the Tcl/Tk GUI toolkit to be installed. You can get this toolkit by making sure the latest X11 application (xQuartz) is installed, see here: https://www.xquartz.org/. More information on installation is found in juicrs's vignette.

Examples

## Not run: 

GUI_juicr(system.file("images", "Kortum_and_Acymyan_2013_Fig4.jpg", package = "juicr"))


## End(Not run)

An example image of a scatterplot figure

Description

A jpg image of a scatterplot from Figure 2 of Kam, M., Cohen-Gross, S., Khokhlova, I.S., Degen, A.A. and Geffen, E. 2003. Average daily metabolic rate, reproduction and energy allocation during lactation in the Sundevall Jird Meriones crassus. Functional Ecology 17:496-503.

Format

A raw jpg-formated image

Note

How to use

readImage(system.file("images", "Kam_et_al_2003_Fig2.jpg", package = "juicr"))

An example image of a bar plot figure

Description

A jpg image of a bar plot from Figure 4 of Kortum, P., and Acymyan, C.Z. 2013. How low can you go? Is the System Usability Scale range restricted? Journal of Usability Studies 9:14-24.

Format

A raw jpg-formated image

Note

How to use

readImage(system.file("images", "Kortum_and_Acymyan_2013_Fig4.jpg", package = "juicr"))