colocr

An R package for conducting co-localization analysis.

Overview

A few R packages are available for conducting image analysis, which is a very wide topic. As a result, some of us might feel at a loss when all they want to do is a simple co-localization calculations on a small number of microscopy images. This package provides a simple straight forward workflow for loading images, choosing regions of interest (ROIs) and calculating co-localization statistics. Included in the package, is a shiny app that can be invoked locally to interactively select the regions of interest in a semi-automatic way. The package is based on the R package imager.

Installing colocr

colocr is available on CRAN and can be installed using

# install from cran
install.packages('colocr')

The package development version is available at github.

# install from github
devtools::install_github('ropensci/colocr')

This package depends on imager which has some external dependencies. The instructions for installing imager can be found here.

Getting started

To get started, load the required packages and the images. The images below are from DU145 cell line and were stained for two proteins; RKIP and LC3. Then, apply the appropriate parameters for choosing the regions of interest using the roi_select. Finally, check the appropriateness of the parameters by highlighting the ROIs on the image.

# load libraries
library(colocr)

# load images
fl <- system.file('extdata', 'Image0001_.jpg', package = 'colocr')
img <- image_load(fl)

# select ROI and show the results
par(mfrow = c(2,2), mar = rep(1, 4))

img %>%
  roi_select(threshold = 90) %>%
  roi_show()

The same can be achieved interactively using an accompanying shiny app. To launch the app run.

run_app()

The reset of the analysis depends on the particular kind of images. Now, colocr implements two simple co-localization statistics; Pearson's Coefficient Correlation (PCC) and the Manders Overlap Coefficient (MOC).

To apply both measures of correlation, we first get the pixel intensities and call roi_test on the merge image.

# calculate co-localization statistics
img %>%
  roi_select(threshold = 90) %>%
  roi_test(type = 'both')

The same analysis and more can be conducted using a web interface for the package available here

Acknowledgement

• The vignette images from Lai Huyen Trang
• The test examples from Colocalization Benchmark Source (CBS)
• The implementation of the co-localization statistics from Dunn et al.

Citation

citation('colocr')