An R package for conducting co-localization analysis.
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
.
The package development version is available at github.
# install from github
devtools::install_github('MahShaaban/colocr')
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
- 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.
browseVignettes('colocr')