2023-CytoPipeline-code

Code and raw data to reproduce the results in the CytoPipeline and CytoPipelineGUI article.

User's instruction:

Set-up

• do a git clone of this github repo

• create a R project pointing to the root directory

• if not done yet, install the needed packages: CytoPipeline, CytoPipelineGUI, pipeComp, and CytoPipelineUtils:

# if (!require("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# 
# BiocManager::install("CytoPipeline")
# BiocManager::install("CytoPipelineGUI")
# BiocManager::install("pipeComp")
#
# if (!require("devtools", quietly = TRUE))
#     install.packages("devtools")
# devtools::install_github(
#     "https://github.com/UCLouvain-CBIO/CytoPipelineUtils/")

Generating the CytoPipeline caches

• Execute the R script : source("./R/1_build_and_run_pipelines.R")

This is likely to take several minutes. Also note that during the run of the first pipeline (HBVMouse_PQC_error experiment), some error messages are encountered, these are expected errors:

Error : BiocParallel errors

55 remote errors, element index: 1, 2, 3, 4, 5, 6, ...

0 unevaluated and other errors

first remote error:

Error in removeDebrisFlowClustTmix(new("flowFrame", exprs = structure(c(401.926147460938, : argument "nClust" is missing, with no default

Generate the pipeComp results

• Execute the R script : source("./R/2_build_and_run_benchmark.R")

This is also likely to take several minutes. Also note that during the run, pipeComp might generate warnings as below, this is not to worry about.

'as.is' should be specified by the caller; using TRUE

Produce the plots in article section : Results/Visual Assessments

• Execute the lines (one by one) of the following R script:
  ./R/3_Results_VisualAssessment.R

Produce the plots in article section : Results/Benchmark results

• Execute the lines (one by one) of the following R script:
  ./R/4_Results_VisualAssessment.R