Merge branch 'master' into test-prepare-experiment

hms-dbmi-cellenics · Oct 8, 2021 · b7b2971 · b7b2971
2 parents 7a27088 + 1c02f3c
commit b7b2971
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Showing 5 changed files with 29 additions and 3 deletions.
diff --git a/pipeline-runner/R/gem2s-6-construct_qc_config.R b/pipeline-runner/R/gem2s-6-construct_qc_config.R
@@ -6,6 +6,7 @@ construct_qc_config <- function(scdata, any_filtered) {
     # classifier
     config.classifier <- list(
         enabled = !any_filtered,
+        prefiltered = any_filtered,
         auto = TRUE,
         filterSettings = list(FDR = 0.01))
 

diff --git a/pipeline-runner/R/qc-4-filter_gene_umi_outlier.R b/pipeline-runner/R/qc-4-filter_gene_umi_outlier.R
@@ -25,8 +25,8 @@
 #'
 filter_gene_umi_outlier <- function(scdata, config, sample_id, task_name = "numGenesVsNumUmis", num_cells_to_downsample = 6000) {
 
-  p.level <- config$filterSettings$regressionTypeSettings[[config$filterSettings$regressionType]]$p.level
-
+  p.level <- suppressWarnings(as.numeric(config$filterSettings$regressionTypeSettings[[config$filterSettings$regressionType]]$p.level))
+  if(is.na(p.level)) stop("P-level couldnt be interpreted as a number.")
   if (as.logical(toupper(config$enabled))) {
     if (config$filterSettings$regressionType == "gam") {
       # Subsetting this sample

diff --git a/pipeline-runner/tests/testthat/test-gem2s-6-construct_qc_config.R b/pipeline-runner/tests/testthat/test-gem2s-6-construct_qc_config.R
@@ -20,8 +20,10 @@ test_that("cellsize filter is disabled by default and classifier if pre-filtered
     scdata <- mock_scdata()
 
     qc_config <- construct_qc_config(scdata, any_filtered = TRUE)
-    expect_false(qc_config$cellSizeDistribution$enabled)
+
     expect_false(qc_config$classifier$enabled)
+    expect_true(qc_config$classifier$prefiltered)
+    expect_false(qc_config$cellSizeDistribution$enabled)
 })
 
 

diff --git a/pipeline-runner/tests/testthat/test-qc-4-filter_gene_umi_outlier.R b/pipeline-runner/tests/testthat/test-qc-4-filter_gene_umi_outlier.R
@@ -85,3 +85,26 @@ test_that("filter_gene_umi_outlier return the appropriate plot data", {
     # is numeric
     expect_equal(class(pdat[[1]]), 'numeric')
 })
+
+test_that("Gene UMI filter works if input is a a float-interpretable string", {
+    scdata <- mock_scdata()
+    config <- mock_config()
+    nstart <- ncol(scdata)
+    config$auto <- FALSE
+    out_number <- filter_gene_umi_outlier(scdata, config, '123def')
+
+    config$filterSettings$regressionTypeSettings$gam$p.level <- "0.1"
+    out_string <- filter_gene_umi_outlier(scdata, config, '123def')
+
+    expect_lt(ncol(out_number$data),nstart)
+    expect_equal(ncol(out_number$data),ncol(out_string$data))
+})
+
+test_that("Gene UMI filter throws error if input is a non float-interpretable string", {
+    scdata <- mock_scdata()
+    config <- mock_config()
+    config$auto <- FALSE
+    config$filterSettings$regressionTypeSettings$gam$p.level <- "asd"
+
+    expect_error(filter_gene_umi_outlier(scdata, config, '123def'))
+})
diff --git a/pipeline-runner/tests/testthat/testthat-problems.rds b/pipeline-runner/tests/testthat/testthat-problems.rds