inst/develo/dockerCelia/runDockerApp.R

In C3BI-pasteur-fr/UTechSCB-SCHNAPPs: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

#' this is used to run the app without installing it.
#'
#'
library(reactlog)
# if (!exists(".schnappsEnv")) {
.schnappsEnv <- new.env(parent=emptyenv())
# }
# 
library(future)

# devtools::install_github("C3BI-pasteur-fr/UTechSCB-SCHNAPPs", dependencies = TRUE)


if(!exists("WORKERS")) WORKERS = parallel::detectCores()


# plan("multiprocess", workers = WORKERS)
plan(sequential)


library("BiocParallel")
register(safeBPParam(WORKERS))
# register(SerialParam())

localContributionDir = "/root/SCHNAPPsContributions/"
# localContributionDir = ""
defaultValueSingleGene = "CDH2" # CD52
defaultValueMultiGenes = "CAV1, MIR205HG, KCNE1B, ANKRD66, SCGB3A2, SCGB3A1, CDH2" # itgae, cd69, itga1" # CD52, S100A9, S100A4
# defaultValueMultiGenes = "prf1, Gzmb, IFNG, PDCD1, HAVCR2, LAG3, TSC22D3,ZFP36L2"
defaultValueRegExGene = "" # tip: '^CD7$|^KIT$; genes with min expression
DEBUG = T
DEBUGSAVE = F
# historyPath = "/Volumes/Oct2020/RStudio_history/"
historyPath = "/root/history"

assign(".SCHNAPPs_locContributionDir", localContributionDir, envir = .schnappsEnv)
assign(".SCHNAPPs_defaultValueSingleGene", defaultValueSingleGene, envir = .schnappsEnv)
assign(".SCHNAPPs_defaultValueMultiGenes", defaultValueMultiGenes, envir = .schnappsEnv)
assign(".SCHNAPPs_defaultValueRegExGene", defaultValueRegExGene, envir = .schnappsEnv)
assign(".SCHNAPPs_DEBUG", DEBUG, envir = .schnappsEnv)
assign(".SCHNAPPs_DEBUGSAVE", DEBUGSAVE, envir = .schnappsEnv)
assign("localContributionDir", localContributionDir, envir = .schnappsEnv)
assign("defaultValueSingleGene", defaultValueSingleGene, envir = .schnappsEnv)
assign("defaultValueMultiGenes", defaultValueMultiGenes, envir = .schnappsEnv)
assign("defaultValueRegExGene", defaultValueRegExGene, envir = .schnappsEnv)
assign("DEBUG", DEBUG, envir = .schnappsEnv)
assign("DEBUGSAVE", DEBUGSAVE, envir = .schnappsEnv)
assign("historyPath", historyPath, envir = .schnappsEnv)
ls(.schnappsEnv)


# # Scran parameters
defaultValues = list()


# Seurat parameters
# defaultValues = list()

# defaultValues[["selectIds"]] = ""
defaultValues[["pcaN"]] = 500
defaultValues[["pcaScale"]] = TRUE
defaultValues[["sampleInput"]] =FALSE
defaultValues[["hvgSelection"]] = "vst"
# defaultValues[["alluiv1"]] = "seurartCluster"
defaultValues[["alluiv2"]] = "dbCluster"
# defaultValues[["tabsetCluster"]] = "seurat_Clustering"
defaultValues[["minGenesGS"]] = 100
defaultValues[["minGenes"]] = 1
defaultValues[["maxGenes"]] = 50000
defaultValues[["seurClustDims"]] = 15
defaultValues[["seurClustk.param"]] = 15
defaultValues[["cellPatternRM"]] = "-s1|-s2"
defaultValues[["gQC_binSize"]] = 200
defaultValues[["selectIds"]] = "^MT-|^RP|^MRP|MALAT1|B2M|EEF1A1"
defaultValues[["selectIds"]] = ""
defaultValues[["whichscLog"]] = "calcLog"
defaultValues[["whichscLog"]] = "disablescEx_log"

defaultValues[["gQC_um_n_neighbors"]] = 20 
defaultValues[["gQC_um_spread"]] = 6 
defaultValues[["gQC_um_local_connectivity"]] = 2
# defaultValues[["useSeuratPCA"]] = TRUE

# defaultValues[["DE_panelplotids"]] = c("CD8A", "CD4", "CD8B", "FCER1G", "CCR7", "GZMK", "FoxP3", "GZMK", "GZMB", "CCR7", "LEF1", "CCL5", "VIM", "CCL5", "TCF7", "NKG7", "LGALs1", "NKG7", "SELL", "CST7", "ANXA2", "CST7", "IL7R", "HLA-DRB1", "KLRG1", "CD27", "CTLA4A")
assign("defaultValues", defaultValues, envir = .schnappsEnv)

devscShinyApp = FALSE
packagePath <<- "/usr/local/lib/R/site-library/SCHNAPPs/app"
source(paste0(packagePath,  "/ui.R"))
source(paste0(packagePath,  "/server.R"))

# app <- shinyApp(ui = scShinyUI, server = scShinyServer, enableBookmarking = "server")
app <- shinyApp(ui = scShinyUI, server = scShinyServer)
options(shiny.reactlog=FALSE)

cat(file= stderr(), system("whoami"))

# options(keep.source=TRUE)
# p <- profvis::profvis({
  runApp(app, host = "0.0.0.0", port = 3838, launch.browser = FALSE)
# })
# htmlwidgets::saveWidget(p, '~/profvis1.html')

# 
# schnapps(Ï
# defaultValueMultiGenes = "IL7R, CCR7,CD14, LYZ ,IL7R, S100A4,MS4A1 ,CD8A,FCGR3A, MS4A7 ,GNLY, NKG7,FCER1A, CST3,PPBP",
# defaultValueSingleGene = "MS4A1", DEBUG=TRUE
# )
# 
# 
# sctkEx = SCtkExperiment(assays=list(counts=as.matrix(assays(scEx)[['counts']]),
#                                     logcounts = as.matrix(assays(scEx)[['logcounts']])),
#                         colData = colData(scEx),
#                         rowData = rowData(scEx))
# singleCellTK(inSCE = sctkEx)
# 
# 
# 
# library(SCHNAPPs)
# schnapps(DEBUG = T, historyPath = "/Volumes/Oct2020/RStudio/history/celia/")
#