[WIP] Add a working environment

Dockerfile.cytofcompensation

@@ -0,0 +1,9 @@
+# Use the official image as a parent image.
+FROM continuumio/miniconda3:4.8.2
+
+# Set the working directory.
+WORKDIR ~
+
+# Run the command inside your image filesystem.
+RUN conda install -c conda-forge mamba
+RUN mamba install -y -c bioconda -c conda-forge bioconductor-catalyst=1.6 r::r-stringr  r-ggpmisc r-data.table r-dtplyr r-ggplot2 bioconductor-flowcore r-tiff r::rstudio r-plotly r-matrixstats r-reshape2 r-raster r-viridis bioconductor-ebimage r-scales r-fields plotly unzip libgfortran r-devtools

README.md

@@ -1,3 +1,4 @@
+RStudio: [![Binder](http://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/BodenmillerGroup/cyTOFcompensation/environment?urlpath=rstudio&filepath=README.md)
 # cyTOF compensation
 
 This repository contains scripts used to reproduce a majority of figures from the paper "Compensation of signal spillover in suspension and imaging mass cytometry" by Stéphane Chevrier\*, Helena L. Crowell\*, Vito R.T. Zanotelli\*, Stefanie Engler, Mark D. Robinson, and Bernd Bodenmiller which is published in 'Cell Systems' as "Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry" (http://www.cell.com/cell-systems/abstract/S2405-4712(18)30063-2)
@@ -8,6 +9,28 @@ The raw data is available from Mendeley data under the DOI code 10.17632/v58yj49
 The CATALYST package developed specifically to allow a user friendly usage of the developped spillover estimation and compensation approach can be found for download at: http://bioconductor.org/packages/CATALYST
 A link to the light version of the web app, installation instructions, example datasets, and vignettes for CATALYST are available from the project page: https://catalyst-project.github.io/. 
 
+
+## Scripts in this repository only works for CATALYST 1.6
+
+Due to changes in CATALYST, this repository only works with older versions (tested: CATALYST 1.6).
+To generate a compatible enviornment, we suggest you to use conda:
+https://docs.conda.io/projects/conda/en/latest/user-guide/install
+
+To install the environment use:
+```
+conda env create -f environment.yml -n cytofcompensation
+conda activate cytofcompensation
+```
+on a desktop you should be able to start Rstudio via
+
+```
+rstudio
+```
+
+This was tested on Ubuntu 18.04.
+Alternatively we provide a dockerfile to generate a container with the environment.
+
+
 The repository is organized in the following scripts:
 
 0) retrieve_data.R:\

environment.yml

@@ -0,0 +1,27 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconductor-catalyst=1.6
+  - r::r-stringr
+  - r-ggpmisc
+  - r-data.table
+  - r-dtplyr
+  - r-ggplot2
+  - bioconductor-flowcore
+  - r-tiff
+  - r::rstudio
+  - r-plotly
+  - r-matrixstats
+  - r-reshape2
+  - r-raster
+  - r-viridis
+  - bioconductor-ebimage
+  - r-scales
+  - r-fields
+  - plotly
+  - r-irkernel
+  - libiconv
+  - icu<=60
+  - libgfortran
+  - r-devtools

scripts/retrieve_data.R

@@ -9,11 +9,11 @@
 #              'https://data.mendeley.com/datasets/v58yj49pfr/draft/files/3ef240f2-96ab-4dd7-aba4-68150c286990/Figure_4.zip?dl=1',
 #              'https://data.mendeley.com/datasets/v58yj49pfr/draft/files/8ac64093-0273-4ae3-a53e-fdb3348ee7ac/Figure_S5.zip?dl=1')
 
-urls_data = c('https://data.mendeley.com/datasets/v58yj49pfr/1/files/4cd060d1-9714-4040-ad24-9aa48b47d520/Figure_1.zip?dl=1',
-              'https://data.mendeley.com/datasets/v58yj49pfr/1/files/eeefe10c-49f8-4dc6-84b5-0fd82c7d9449/Figure_2-3.zip?dl=1',
-              'https://data.mendeley.com/datasets/v58yj49pfr/1/files/75c2eea3-0bca-4c7d-a06a-c0a75ebebcd2/Figure_4.zip?dl=1',
-              'https://data.mendeley.com/datasets/v58yj49pfr/1/files/859158e7-2786-481e-b070-99aab43aba36/Figure_S3.zip?dl=1',
-              'https://data.mendeley.com/datasets/v58yj49pfr/1/files/0e52746f-545c-4607-91c2-cd8635d4d269/Figure_S5.zip?dl=1')
+urls_data = c('https://data.mendeley.com/public-files/datasets/v58yj49pfr/files/cd2b59f9-b34a-46c3-af33-fe3c43ed7d80/file_downloaded?dl=1',
+              'https://data.mendeley.com/public-files/datasets/v58yj49pfr/files/758f4f06-730e-4046-9b65-4ce74c56f581/file_downloaded?dl=1',
+              'https://data.mendeley.com/public-files/datasets/v58yj49pfr/files/fad34c02-8a26-4291-814a-dc3bd4d980a2/file_downloaded?dl=1',
+              'https://data.mendeley.com/public-files/datasets/v58yj49pfr/files/2eb186ee-7410-4f2e-b42e-1d2d8b8b4931/file_downloaded?dl=1',
+              'https://data.mendeley.com/public-files/datasets/v58yj49pfr/files/b39223d2-2825-4e79-9875-86fa0e1c55d2/file_downloaded?dl=1')
 
 # set working directory to current script location
 scriptdir <- dirname(parent.frame(2)$ofile)

scripts/spillover_imc_helpers.R

@@ -219,9 +219,9 @@ comp_datimg <- function(datimg, sm, method='nnls',...){
 
   img_comp = img_mat %>%
     flowCore::flowFrame() %>%
-    CATALYST::compCytof(sm,method=method, ...) %>%
+    CATALYST::compCytof(as.matrix(sm),method=method, ...) %>%
     flowCore::exprs() %>%
     as.data.table()
   setnames(img_comp, orig_names)
   return(img_comp)
-} 
+}