Code and raw data to reproduce the results in the CytoPipeline and CytoPipelineGUI article.
User's instruction:
-
do a
git cloneof 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/")
- 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
- 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
- Execute the lines (one by one) of the following R script:
./R/3_Results_VisualAssessment.R
- Execute the lines (one by one) of the following R script:
./R/4_Results_VisualAssessment.R