[bug] Error with UMAP plot generation

[vd4mmind]

Describe the bug Unable to run the steps in the Vigenette. Section Step four – Merging multiple datasets into one SingleCellExperiment object

To Reproduce Steps to reproduce the behavior:

1. In R:

.sce_list <- list()

for(i in dir_list){
  mat <- read_sparse_matrix(i)
  metadata <- read_metadata(
    unique_key = manifest$key[as.numeric(gsub("individual_", "", basename(i)))],
    key_colname = "manifest",
    samplesheet_path = samplesheet_fp
  )
  var_classes <- c(
    individual = "factor"
  )
  metadata <- read_metadata(
    unique_key = manifest$key[as.numeric(gsub("individual_", "", basename(i)))],
    key_colname = "manifest",
    samplesheet_path = samplesheet_fp,
    col_classes = var_classes
  )
  sce <- generate_sce(mat, metadata)
  sce <- annotate_sce(
    sce,
    ensembl_mapping_file = ensembl_fp
  )
  sce <- filter_sce(sce)
  sce <- find_singlets(sce, "doubletfinder", pK = 0.005, 
                        vars_to_regress_out = c("nCount_RNA", "pc_mito"), 
                        num.cores = 1)
  sce <- filter_sce(sce)
  outdir <- file.path(outputDir,"/scflow_vignette_data")
  dir.create(outdir, showWarnings = FALSE)
  
  dir_report <- file.path(outdir, "qc_report")
  dir.create(dir_report, showWarnings = FALSE)
  
  #report_qc_sce(sce, report_file = paste0("qc_report_", basename(i)),
  #              report_folder_path = dir_report)
  
  sce_list[[basename(i)]] <- sce
  
}

sce <- merge_sce(
  sce_list,
  ensembl_mapping_file = ensembl_fp
)

3. See error:

→ Calculating tSNE reduced dimensions
→ Calculating UMAP reduced dimensions
Error in RunUMAP.default(object = data.use, reduction.model = reduction.model,  : 
  lazy-load database '/home/sagemaker-user/R/x86_64-pc-linux-gnu-library/4.2/uwot/R/uwot.rdb' is corrupt
In addition: Warning messages:
1: In RunUMAP.default(object = data.use, reduction.model = reduction.model,  :
  restarting interrupted promise evaluation
2: In RunUMAP.default(object = data.use, reduction.model = reduction.model,  :
  internal error -3 in R_decompress1](url)
**Expected behavior**
Creation of the report with corresponding plots.

System

R version 4.2.3 (2023-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS

[vd4mmind]

The above is solved but I am having the below issue with the UMAP plots. Seems like very redundant and a problem with ggplot2. Not a clear solution found yet. Any specific package that I should remove?

plot_reduced_dim(sce, feature_dim = "diagnosis", 
                 reduced_dim = "UMAP_Liger", alpha = 1, size = 1)

Error Error in as.unit(e1) : object is not coercible to a unit