diff --git a/DESCRIPTION b/DESCRIPTION index 0c2caf92ed9440d7b192ee8228185b8f4d22b8de..dcfea8dfe4716768a7a1886896b962f8aafcd47d 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: SCHNAPPs Type: Package Title: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data -Version: 1.12.47 +Version: 1.12.48 Authors@R: c(person("Bernd", "Jagla", role = c("aut", "cre"), email = "bernd.jagla@pasteur.fr", comment = c(ORCID = "0000-0002-7696-0484"))) Maintainer: Bernd Jagla <bernd.jagla@pasteur.fr> Description: Single Cell sHiny APPlication (SCHNAPPs) is a R/Shiny based application to interact, manipulate, explore, and analyze single cell RNA-seq experiments, including MARS-seq and others. diff --git a/inst/app/contributions/DE_DataExploration/reactives.R b/inst/app/contributions/DE_DataExploration/reactives.R index 6a9194ec264119065df0c5e2c6e66ae5ebdc86c4..7e9cc6c579441dc65f2be9e0f4bd52f294d19f8e 100644 --- a/inst/app/contributions/DE_DataExploration/reactives.R +++ b/inst/app/contributions/DE_DataExploration/reactives.R @@ -566,5 +566,6 @@ panelPlotFunc <- function(scEx_log, projections, genesin, dimx4, dimy4, sameScal ) return(retVal) } +# panelPlotFunc_m = memoise::memoise(panelPlotFunc,cache=do.call(cachem::cache_disk,.schnappsEnv$cacheDir)) panelPlotFunc_m = panelPlotFunc diff --git a/inst/app/contributions/gQC_generalQC/reactives.R b/inst/app/contributions/gQC_generalQC/reactives.R index 3b6fd1561105a5a1c68854ac036ac7761bfa1e57..92f6f37f089ab98ff9af4dfda8ea595df0c59df8 100644 --- a/inst/app/contributions/gQC_generalQC/reactives.R +++ b/inst/app/contributions/gQC_generalQC/reactives.R @@ -649,5 +649,9 @@ if("DoubletFinder" %in% installed.packages()){ # colnames(result) = c("DF.score", "DF.class") return(result) } + # if("DoubletFinder" %in% installed.packages()){ + # find_doublets_m <- memoise::memoise(find_doublets,cache=do.call(cachem::cache_disk,.schnappsEnv$cacheDir)) + find_doublets_m <- find_doublets + # find_doublets_m <- memoise::memoise(find_doublets,cache=do.call(cachem::cache_disk,.schnappsEnv$cacheDir)) } \ No newline at end of file diff --git a/inst/app/contributions/sCA_subClusterAnalysis/reactives.R b/inst/app/contributions/sCA_subClusterAnalysis/reactives.R index 7d79f7fc94a78a9b05dbdf04d8b70fbf0cf5839b..02425fc4962d2790cb764cacbaf391f6175dab1b 100644 --- a/inst/app/contributions/sCA_subClusterAnalysis/reactives.R +++ b/inst/app/contributions/sCA_subClusterAnalysis/reactives.R @@ -222,6 +222,8 @@ sCA_seuratFindMarkers <- function(scEx, cells.1, cells.2, test="wilcox", normFac } return(markers) } +# sCA_seuratFindMarkers_m = memoise::memoise(sCA_seuratFindMarkers,cache=do.call(cachem::cache_disk,.schnappsEnv$cacheDir)) +sCA_seuratFindMarkers_m = sCA_seuratFindMarkers sCA_dge_s_wilcox <- function(scEx_log, cells.1, cells.2){ @@ -414,6 +416,7 @@ runDESEQ2 <- function(data.use, group.info) { } # runDESEQ2_m <- memoise::memoise(runDESEQ2,cache=do.call(cachem::cache_disk,.schnappsEnv$cacheDir)) sCA_seuratFindMarkers_m = sCA_seuratFindMarkers +runDESEQ2_m <- runDESEQ2 sCA_dge_deseq2 <- function(scEx_log, cells.1, cells.2) { diff --git a/inst/app/contributions/traj_trajectories/reactives.R b/inst/app/contributions/traj_trajectories/reactives.R index 3d8d830cf5f9a4e38e8af9cba564a61e6b61e2f9..6dc3d69628644a09e244ca8e7359d879542cdb45 100644 --- a/inst/app/contributions/traj_trajectories/reactives.R +++ b/inst/app/contributions/traj_trajectories/reactives.R @@ -274,12 +274,12 @@ if (!is.null(.schnappsEnv$enableTrajectories)) { # it is possible that after reloading a workspace under some circumstances the underlying data changed if(!all(rownames(traj) %in% colnames(scEx_log))) return(NULL) - # cellsNotFound <- colnames(assays(scEx_log)[[1]])[!colnames(assays(scEx_log)[[1]]) %in% rownames(traj)] - # dig = digest(list(assays(scEx_log)[[1]][,rownames(traj)], traj$time, scorpRepeat), algo = "sha256") - # if(!is.null(.schnappsEnv$react.scorpiusExpSel)) - # if(dig == .schnappsEnv$react.scorpiusExpSel[[1]]) { - # return(.schnappsEnv$react.scorpiusExpSel[[2]]) - # } + cellsNotFound <- colnames(assays(scEx_log)[[1]])[!colnames(assays(scEx_log)[[1]]) %in% rownames(traj)] + dig = digest(list(assays(scEx_log)[[1]][,rownames(traj)], traj$time, scorpRepeat), algo = "sha256") + if(!is.null(.schnappsEnv$react.scorpiusExpSel)) + if(dig == .schnappsEnv$react.scorpiusExpSel[[1]]) { + return(.schnappsEnv$react.scorpiusExpSel[[2]]) + } regis=registered()[[1]] workers = ifelse("workers" %in% names(regis), regis$workers, detectCores()) expression <- t(as.matrix(assays(scEx_log)[[1]][,rownames(traj)])) diff --git a/inst/app/reactives.R b/inst/app/reactives.R index 71c7152e3fc2c506ef28bfd757c0312827fc735a..c46b00fb7a6635b236b7fc38f864b20ebf0f63f5 100644 --- a/inst/app/reactives.R +++ b/inst/app/reactives.R @@ -2417,18 +2417,12 @@ runSeuratClustering <- function(scEx, meta.data, dims, pca, k.param, resolution) # heatmapModuleFunction_m = heatmapModuleFunction # runSeuratClustering_m <- memoise::memoise(runSeuratClustering,cache=do.call(cachem::cache_disk,.schnappsEnv$cacheDir)) # panelPlotFunc_m = memoise::memoise(panelPlotFunc,cache=do.call(cachem::cache_disk,.schnappsEnv$cacheDir)) +# scranCluster_m <- memoise::memoise(scranCluster,cache=do.call(cachem::cache_disk,.schnappsEnv$cacheDir)) + # -# if("DoubletFinder" %in% installed.packages()){ -# find_doublets_m <- memoise::memoise(find_doublets,cache=do.call(cachem::cache_disk,.schnappsEnv$cacheDir)) # } -# sCA_seuratFindMarkers_m = memoise::memoise(sCA_seuratFindMarkers,cache=do.call(cachem::cache_disk,.schnappsEnv$cacheDir)) # } else { -runSeuratClustering_m <- runSeuratClustering -# runDESEQ2_m <- runDESEQ2 -if("DoubletFinder" %in% installed.packages()){ - find_doublets_m <- find_doublets -} # seurat_Clustering <- function() { diff --git a/inst/develo/dockerImage/Dockerfile b/inst/develo/dockerImage/Dockerfile index 73937addbfcfca7de63e95cd5296b2d70b457d66..3f4cd202ae93a36c3a48ce46b4428fc469f441ab 100644 --- a/inst/develo/dockerImage/Dockerfile +++ b/inst/develo/dockerImage/Dockerfile @@ -82,10 +82,8 @@ RUN R -e "devtools::install_github('Albluca/distutils') " && \ R -e "BiocManager::install('BiocParallel')" && \ R -e "remotes::install_github('briatte/ggnetwork')" \ R -e "devtools::install_github('theislab/destiny', dependencies = TRUE)" -RUN R -e "devtools::install_github('C3BI-pasteur-fr/UTechSCB-SCHNAPPs', dependencies = TRUE)" - #RUN apt-get update && apt-get install -y pandoc-citeproc RUN R -e "BiocManager::install(c('InteractiveComplexHeatmap'))" -#RUN R -e "setRepositories(ind = c(1,2,3));devtools::install_github('RausellLab/CelliD', ref = 'legacy')" +RUN R -e "devtools::install_github('C3BI-pasteur-fr/UTechSCB-SCHNAPPs', dependencies = TRUE)" RUN sudo apt-get update -y; sudo apt-get install -y r-cran-rcppeigen RUN R -e "devtools::install_github('mul118/shinyMCE')"