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

knitr::opts_chunk$set(echo = TRUE)
source("~/Rstudio/UTechSCB-SCHNAPPs/inst/app/serverFunctions.R", echo=F)

doCalc <- input$scorpiusCalc

# "dimScorpiusX" %in% names(.schnappsEnv$defaultValues)
# "dimScorpiusY" %in% names(.schnappsEnv$defaultValues)
# .schnappsEnv$defaultValues[["dimScorpiusX"]]
# .schnappsEnv$defaultValues[["dimScorpiusY"]]
# "elpiStartNode" %in% names(.schnappsEnv$defaultValues)
# 
# res2 = coE_somTrainReact()
# scEx <- isolate(scEx())
# scEx_log <- isolate(scEx_log())
# prjs <- isolate(sessionProjections$prjs)
# projFactors <- projFactors()
# projections <- isolate(projections())
# inp = reactiveValuesToList(input)
# somInputData = somInputData()
# coE_somMapReact = coE_somMapReact()
# coE_somTrainReact = coE_somTrainReact()
# coE_somGenesReact = coE_somGenesReact()
# coE_heatmapSOMReactive = coE_heatmapSOMReactive()

genesin <- input$coE_geneSOM

featureData <- rowData(scEx_log)
geneName = geneName2Index(genesin, featureData)

# coE_SOMcodebook = output$coE_SOMcodebook()
endpoints <- traj_endpoints()
save(file = "test.RData", list = c(ls(),".schnappsEnv"))

umapData <- as.matrix(assays(scEx_log)[[1]])
compCases <- complete.cases(umapData)
save(file = "embedding.Rdata", list=c(ls()))
# cp = load("embedding.Rdata")
library(ggplot2)
# for (n_neighbors in seq(2,100,by =10)){
#   for(spread in seq( 2,20, by=3)){
#   for(min_dist in seq(0.01, 0.5, by = 0.08)){
#     for (local_connectivity in seq(1, 20, by = 5)){
for (n_neighbors in c(2,50,100)){
  for(spread in c( 2,5,10,20)){
    for(min_dist in c(0.01, 0.2, 0.5)){
      for (local_connectivity in c(1, 5, 10, 20)){
        embedding <- tryCatch(uwot::umap(pca$x  ,
                                n_neighbors = n_neighbors,
                                n_components = 3,
                                n_epochs = 2000,
                                # alpha = alpha,
                                init = "spectral",
                                spread = spread,
                                min_dist = min_dist,
                                set_op_mix_ratio = 1,
                                local_connectivity = local_connectivity,
                                bandwidth = 1,
                                # gamma = gamma,
                                negative_sample_rate = 5,
                                metric = "cosine",
                                n_threads = 8
        ), error = function(x)return(NULL))
        if(is.null(embedding)) next()
        embedding <- as.data.frame(embedding)
        colnames(embedding) <- paste0("UMAP", 1:3)
        rownames(embedding) <- colnames(scEx_log)
        embedding$dbCluster = projections[rownames(embedding), "dbCluster"]
        print(ggplot(embedding, aes(x=UMAP1, y=UMAP2, color=dbCluster)) + geom_point() + 
              ggtitle(paste("n_neighbors:", n_neighbors, " spread:", spread, " min_dist:", min_dist, " local_connectivity:", local_connectivity))
        )
      }
    }
  }
}
#   embedding <- as.data.frame(embedding)
#   colnames(embedding) <- paste0("UMAP", 1:n_components)
#   rownames(embedding) <- colnames(scEx_log)
# save(file = "embedding.Rdata", list=c(ls()))

C3BI-pasteur-fr/UTechSCB-SCHNAPPs documentation built on Jan. 12, 2025, 1:16 p.m.