neighbouRhood
Adds an R implementation for the HistoCAT neightbourhood analysis (https://www.nature.com/articles/nmeth.4391) that runs from 'CellProfiler output' or 'CellProfiler output'-like data.
Data requirements
This require an edge representation of a neightbourhood graph as well as a table that associates each object with a label.
The neightbourhood graph can be exported from object segmentation masks via the Object relationships.csv
table.
To do this use the MeasureObjectNeighbors
module and add an additional ExportToSpreadsheet
module with the option Export all measurement types -> No
and select Object Relationships
.
Further it needs a table which associates each of the measured oject (with ImageNumber
and ObjectNumber
) with a label
(eg a cluster).
Installation
Either clone and install the repository or install devtools
to run:
devtools::install_github("BodenmillerGroup/neighbouRhood")
Documentation
Please follow the vignette https://github.com/BodenmillerGroup/neighbouRhood/blob/master/vignettes/example_permutation_analysis.md
to see an explaination about the concept behind the package and how to use it.
Also all individual functions are documented, ie the documentation can be displayed using: ?neightbouRhood
.
Support
In case you need help, please open a Github issue!