Small changes before release

[ktrns]

I figured that for my projects it is helpful to plot QC again after we filtered based on the given thresholds. I'd like to include this into the main scrnaseq.Rmd.

Edit 23.2.22: done

[ktrns]

Double-check chunk headers

Edit 23.2.22: done

[ktrns]

Table Number of cells per sample and cluster: column names = clusters are not sorted

Edit 23.2.22: done

[ktrns]

UPDATE: We changed this back to the original. We need to consider both values, but not systematically like below. More of a visual inspection of the QC scatter plots.

---

QC-filter cells only if they break all numeric filters, e.g. more than 20% mitochondrial reads AND less than 500 genes. Citation from the best practice paper:

"[...], cells with a comparatively high fraction of mitochondrial counts may be involved in respiratory processes. Likewise, other QC covariates also have biological interpretations. Cells with low counts and/or genes may correspond to quiescent cell populations, and cells with high counts may be larger in size. Indeed, molecular counts can differ strongly between cells [...]. Thus, QC covariates should be considered jointly when univariate thresholding decisions are made [...], and these thresholds should be set as permissive as possible to avoid filtering out viable cell populations unintentionally."

Solution in chunk filter_cells:

  filter_result_sep = purrr::map(list_names(param$cell_filter[[n]]), function(f) {
    filter = param$cell_filter[[n]][[f]]
    if (is.numeric(filter)) {
      if (is.na(filter[1])) filter[1] = -Inf # Minimum
      if (is.na(filter[2])) filter[2] = Inf  # Maximum 
      idx_exclude = sc[[n]][[f, drop=TRUE]] < filter[1] | sc[[n]][[f, drop=TRUE]] > filter[2]
      return(names(which(idx_exclude)))
    } else if (is.character(filter)) { 
      idx_exclude = !sc[[n]][[f, drop=TRUE]] %in% filter
      return(Cells(sc[[n]])[idx_exclude])
    }
  })

  filter_result = list()
  filter_result$qc_jointly = filter_result_sep %>% purrr::reduce(.f=intersect)

[ktrns]

Update docs/*.md on how to run the pipelines

Edit 23.2.22: added a separate #112

[ktrns]

Solve #73 - add a point to the main README.md

Edit 23.2.22: done

[ktrns]

@andpet0101 fixed a range of small bugs:

• Don't use param and params in the script
• Add hostname to the output
• Catch the fact that the script breaks if only one cluster is found
• issue #111
• issue #108
• typos percent_ercc & print(p) in if statement
• added k parameter to control for k in clustering and umap visualisation

Open issues:

• Figure heights for cluster tests
• Edit 24.2.22: done