parametrize the operator that joins cell QC filters (| or &) (#7)

gorgitko · web-flow · commit 9bdf431975d7 · 2023-12-18T16:36:26.000+01:00
* parametrize the operator that joins cell QC filters (| or &amp;)

* use AND/OR in docs

* validate DATASET_SENSITIVE_FILTERS_OPERATOR and CUSTOM_FILTERS_OPERATOR

* bump version, update README
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: scdrake
 Type: Package
 Title: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language
-Version: 1.5.1
+Version: 1.5.2
 Authors@R:
     c(
       person(
diff --git a/NAMESPACE b/NAMESPACE
@@ -100,6 +100,7 @@ export(get_single_sample_plan)
 export(get_sys_env)
 export(get_tmp_dir)
 export(get_top_hvgs)
+export(get_used_qc_filters_operator_desc)
 export(get_yq_default_path)
 export(glue0)
 export(glue0c)
diff --git a/R/config_process_single_sample.R b/R/config_process_single_sample.R
@@ -29,6 +29,15 @@
     msg = "{.var input_data$type} must be {.vals possible_input_data_types}. Current value: {.val {cfg$INPUT_DATA$type}}"
   )
 
+  possible_filters_operators <- c("&", "|")
+  for (param_name in c("DATASET_SENSITIVE_FILTERS_OPERATOR", "CUSTOM_FILTERS_OPERATOR")) {
+    val <- cfg[[param_name]]
+    assert_that_(
+      val %in% possible_filters_operators,
+      msg = "{.field {param_name}} must be one of {.vals {possible_filters_operators}}. Current value: {.val {val}}"
+    )
+  }
+
   assert_that_(
     !is_null(cfg$INPUT_DATA$path),
     msg = "{.field INPUT_DATA$type} is not set, data cannot be loaded later."
diff --git a/R/plans_single_sample.R b/R/plans_single_sample.R
@@ -60,7 +60,7 @@ get_input_qc_subplan <- function(cfg, cfg_pipeline, cfg_main) {
     ),
     qc_filters = purrr::map(qc_filters_raw, ~ as.logical(.) %>% tidyr::replace_na(replace = FALSE)),
     ## -- Join filters by OR operator.
-    qc_filter = Reduce("|", qc_filters),
+    qc_filter = Reduce(!!cfg$DATASET_SENSITIVE_FILTERS_OPERATOR, qc_filters),
 
     ## -- Custom filters.
     custom_filters_raw = list(
@@ -71,7 +71,7 @@ get_input_qc_subplan <- function(cfg, cfg_pipeline, cfg_main) {
       # low_ribo = cell_qc$subsets_ribo_percent <= !!cfg$MIN_RIBO_RATIO * 100
     ),
     custom_filters = purrr::map(custom_filters_raw, ~ as.logical(.) %>% tidyr::replace_na(replace = FALSE)),
-    custom_filter = Reduce("|", custom_filters),
+    custom_filter = Reduce(!!cfg$CUSTOM_FILTERS_OPERATOR, custom_filters),
 
     ## -- Add filters to sce and create Seurat object.
     sce_unfiltered = sce_add_colData(
diff --git a/R/single_sample_input_qc.R b/R/single_sample_input_qc.R
@@ -263,3 +263,19 @@ sce_final_input_qc_fn <- function(sce_selected, gene_annotation) {
 
   return(sce_final_input_qc)
 }
+
+#' Return an informative message about the used operator to join cell QC filters
+#'
+#' @param operator A character scalar: used operator.
+#'
+#' @return A character scalar: the message
+#'
+#' @concept single_sample_input_qc_fn
+#' @export
+get_used_qc_filters_operator_desc <- function(operator = c("&", "|")) {
+  if (operator == "&") {
+    "Individual filters were considered jointly (using *AND* operator), i.e., a cell was removed only if violated all of the filters."
+  } else {
+    "Individual filters were considered individually (using *OR* operator), i.e., a cell was removed if violated at least one filter."
+  }
+}
diff --git a/README.md b/README.md
@@ -108,8 +108,8 @@ You can pull the Docker image with the latest stable `{scdrake}` version
 using
 
 ``` bash
-docker pull jirinovo/scdrake:1.5.1
-singularity pull docker:jirinovo/scdrake:1.5.1
+docker pull jirinovo/scdrake:1.5.2
+singularity pull docker:jirinovo/scdrake:1.5.2
 ```
 
 or list available versions in [our Docker Hub
@@ -151,7 +151,7 @@ docker run -d \
   -e USERID=$(id -u) \
   -e GROUPID=$(id -g) \
   -e PASSWORD=1234 \
-  jirinovo/scdrake:1.5.1
+  jirinovo/scdrake:1.5.2
 ```
 
 For Singularity, also make shared directories and execute the container
@@ -234,7 +234,7 @@ for `{scdrake}` and you can use it to install all dependencies by
 
 ``` r
 ## -- This is a lockfile for the latest stable version of scdrake.
-download.file("https://raw.githubusercontent.com/bioinfocz/scdrake/1.5.1/renv.lock")
+download.file("https://raw.githubusercontent.com/bioinfocz/scdrake/1.5.2/renv.lock")
 ## -- You can increase the number of CPU cores to speed up the installation.
 options(Ncpus = 2)
 renv::restore(lockfile = "renv.lock", repos = BiocManager::repositories())
@@ -254,7 +254,7 @@ installed from the lockfile).
 
 ``` r
 remotes::install_github(
-  "bioinfocz/scdrake@1.5.1",
+  "bioinfocz/scdrake@1.5.2",
   dependencies = FALSE, upgrade = FALSE,
   keep_source = TRUE, build_vignettes = TRUE,
   repos = BiocManager::repositories()
@@ -321,7 +321,7 @@ vignette](https://bioinfocz.github.io/scdrake/articles/scdrake.html)
 ## Vignettes and other readings
 
 See <https://bioinfocz.github.io/scdrake> for a documentation website of
-the latest stable version (1.5.1) where links to vignettes below become
+the latest stable version (1.5.2) where links to vignettes below become
 real :-)
 
 See <https://bioinfocz.github.io/scdrake/dev> for a documentation
diff --git a/inst/Rmd/single_sample/01_input_qc_children/cell_filtering_custom.Rmd b/inst/Rmd/single_sample/01_input_qc_children/cell_filtering_custom.Rmd
@@ -1,7 +1,9 @@
-Filter dataset based on custom (fixed) thresholds of QC metrics:
+Filter cells based on custom (fixed) thresholds of QC metrics:
 
 - &lt;Min; Max&gt; UMI per cell: &lt;`r cfg$MIN_UMI_CF`; `r as.character(cfg$MAX_UMI_CF)`&gt;
 - Min. number of features (genes) detected: `r cfg$MIN_FEATURES`
 - Max. ratio of mitochondrial genes expression: `r cfg$MAX_MITO_RATIO`
 
+`r get_used_qc_filters_operator_desc(cfg$CUSTOM_FILTERS_OPERATOR)`
+
 **Removing `r sum(custom_filter)` low quality cells based on custom thresholds.**
diff --git a/inst/Rmd/single_sample/01_input_qc_children/cell_filtering_qc.Rmd b/inst/Rmd/single_sample/01_input_qc_children/cell_filtering_qc.Rmd
@@ -4,4 +4,6 @@ Filter cells based on QC metrics and MAD threshold (`r cfg$MAD_THRESHOLD`):
 - Low number of detected genes (lower tail).
 - High expression of mitochondrial genes (upper tail).
 
+`r get_used_qc_filters_operator_desc(cfg$CUSTOM_FILTERS_OPERATOR)`
+
 **Removing `r sum(qc_filter)` low quality cells based on MAD.**
diff --git a/inst/Rmd/single_sample/01_input_qc_children/gene_filtering_qc.Rmd b/inst/Rmd/single_sample/01_input_qc_children/gene_filtering_qc.Rmd
@@ -13,7 +13,7 @@ janitor::tabyl(sce_qc_filter_rowSums == 0) %>%
 **Removing `r sum(drake::readd(sce_qc_gene_filter, path = drake_cache_dir))` genes with UMI per cell less than
 `r cfg$MIN_UMI` and expressed in less than `r cfg$MIN_RATIO_CELLS * 100` % of all cells.**
 
-Info on filtered dataset:
+Info on dataset-sensitive filtered dataset:
 
 ```{r}
 cat(drake::readd(sce_qc_filter_genes_info, path = drake_cache_dir)$str)
diff --git a/inst/config/single_sample/01_input_qc.default.yaml b/inst/config/single_sample/01_input_qc.default.yaml
@@ -30,13 +30,15 @@ SAVE_DATASET_SENSITIVE_FILTERING: True
 
 ### Dataset-sensitive cell filtering ##########################################
 MAD_THRESHOLD: 3
+DATASET_SENSITIVE_FILTERS_OPERATOR: "&"
 ###############################################################################
 
 ### Custom cell filtering #####################################################
 MIN_UMI_CF: 1000
 MAX_UMI_CF: 50000
 MIN_FEATURES: 1000
 MAX_MITO_RATIO: 0.2
+CUSTOM_FILTERS_OPERATOR: "&"
 ###############################################################################
 
 ### Gene filtering ############################################################
diff --git a/man/get_used_qc_filters_operator_desc.Rd b/man/get_used_qc_filters_operator_desc.Rd
diff --git a/vignettes/stage_input_qc.Rmd b/vignettes/stage_input_qc.Rmd
@@ -55,8 +55,8 @@ More information about scRNA-seq quality control can be found in
      For "number of UMI" metric, only a lower tail is used.
   - Custom filtering, based on fixed thresholds. For "number of UMI" metric, both upper and lower bounds are used
     ([theory](https://bioconductor.org/books/3.15/OSCA.basic/quality-control.html#fixed-qc).
-  - In both filtering types, violation of only one metric threshold leads to removal of a cell.
-    More technically, metric filters are reduced by **or** operator.
+  - For both filtering types you can choose how to join the filters: either jointly (using the *AND* operator) or
+    individually (using the *OR* operator).
 - Gene filtering (optional) based on a minimum number of UMI per cell and a minimum ratio of cells expressing a gene.
   - A gene is considered expressed when number of its UMI across all cells is greater than X and
     at the same time it is expressed in at least Y ratio of cells.
@@ -245,6 +245,19 @@ Violation of only one metric threshold leads to removal of a cell.
 To disable the dataset-sensitive filtering, set `MAD_THRESHOLD: .inf`.
 That will force passing of each cell as every QC metric will be always lower than positive infinity MAD.
 
+***
+
+```yaml
+DATASET_SENSITIVE_FILTERS_OPERATOR: "&"
+```
+
+**Type:** a character scalar (`"&" | "|"`)
+
+How to join the QC filters:
+
+- Jointly (*AND*/`&` operator), i.e., remove only cells that violate **ALL** filters (permissive)
+- Individually (*OR*/`|` operator), i.e., remove cells that violate **AT LEAST ONE** filter (strict)
+
 ##### Custom cell filtering
 
 ```yaml
@@ -295,6 +308,19 @@ i.e. cells with mitochondrial genes detected in more than (`MAX_MITO_RATIO` * 10
 
 To disable this filter, set `MAX_MITO_RATIO: .inf`
 
+***
+
+```yaml
+CUSTOM_FILTERS_OPERATOR: "&"
+```
+
+**Type:** a character scalar (`"&" | "|"`)
+
+How to join the QC filters:
+
+- Jointly (*AND*/`&` operator), i.e., remove only cells that violate **ALL** filters (permissive)
+- Individually (*OR*/`|` operator), i.e., remove cells that violate **AT LEAST ONE** filter (strict)
+
 #### Gene filtering
 
 Gene filtering thresholds are applied in both types of cell filtering (after it is performed).
