Merge pull request #139 from omnideconv/fix_consensusTME_bug

Fix consensus tme bug (#133) + Cibersort warning (#137)
omnideconv · Mar 9, 2023 · 8282446 · 8282446
2 parents 28fce56 + 6b49224
commit 8282446
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Showing 6 changed files with 32 additions and 5 deletions.
diff --git a/.github/workflows/test-coverage.yml b/.github/workflows/test-coverage.yml
@@ -29,6 +29,13 @@ jobs:
           extra-packages: any::covr
           needs: coverage
 
+      - name: Manually install preprocessCore
+        if: ${{ !(matrix.config.os == 'windows-latest' || matrix.config.os == 'macOS-latest') }}
+        run: |
+          git clone https://github.com/bmbolstad/preprocessCore.git
+          cd preprocessCore
+          R CMD INSTALL --configure-args="--disable-threading"  .
+
       - name: Test coverage
         run: covr::codecov(quiet = FALSE)
         shell: Rscript {0}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -24,7 +24,6 @@ jobs:
           - { os: windows-latest, r: "release" }
           - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
           - { os: ubuntu-latest, r: "release" }
-          - { os: ubuntu-latest, r: "oldrel-1" }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -46,6 +45,13 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
+      - name: Manually install preprocessCore
+        if: ${{ !(matrix.config.os == 'windows-latest' || matrix.config.os == 'macOS-latest') }}
+        run: |
+          git clone https://github.com/bmbolstad/preprocessCore.git
+          cd preprocessCore
+          R CMD INSTALL --configure-args="--disable-threading"  .
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -65,4 +65,4 @@ Roxygen: list(markdown = TRUE)
 LazyData: true
 URL: https:/omnideconv.org/immunedeconv, https://github.com/omnideconv/immunedeconv
 BugReports: https://github.com/omnideconv/immunedeconv/issues
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
diff --git a/R/immune_deconvolution_methods.R b/R/immune_deconvolution_methods.R
@@ -257,7 +257,7 @@ deconvolute_cibersort <- function(gene_expression_matrix,
   source(get("cibersort_binary", envir = config_env))
 
   tmp_mat <- tempfile()
-  write_tsv(as_tibble(gene_expression_matrix, rownames = "gene_symbol"), path = tmp_mat)
+  write_tsv(as_tibble(gene_expression_matrix, rownames = "gene_symbol"), file = tmp_mat)
 
   arguments <- dots_list(get("cibersort_mat", envir = config_env), tmp_mat,
     perm = 0,
@@ -309,6 +309,7 @@ deconvolute_consensus_tme <- function(gene_expression_matrix,
                                       method = "ssgsea",
                                       ...) {
   indications <- toupper(indications)
+  indications[indications == "UNFILTERED"] <- "Unfiltered"
   assert("indications fit to mixture matrix", length(indications) == ncol(gene_expression_matrix))
 
   gene_expression_matrix <- as.matrix(gene_expression_matrix)

diff --git a/tests/testthat/test_deconvolution.R b/tests/testthat/test_deconvolution.R
@@ -97,6 +97,19 @@ test_that("consensus_tme with multiple indications, ordered and unordered", {
 })
 
 
+test_that("consensus_tme with multiple indications, including 'Unfiltered'", {
+  indications_1 <- c("blca", "blca", "brca", "brca", "chol", "chol", "Unfiltered", "Unfiltered")
+  indications_2 <- c("brca", "Unfiltered", "brca", "blca", "Unfiltered", "chol", "chol", "blca")
+  res_1 <- deconvolute_consensus_tme(test_mat, indications = indications_1)
+  res_2 <- deconvolute_consensus_tme(test_mat, indications = indications_2)
+  assert("matrix dimensions consistent", ncol(res_1) == ncol(test_mat))
+  assert("matrix dimensions consistent", ncol(res_2) == ncol(test_mat))
+
+  order.samples <- order(toupper(indications_2))
+
+  assert("proper results", all(colnames(res_1)[order.samples] == colnames(res_2)))
+})
+
 test_that("generic deconvolution works for all methods", {
   lapply(deconvolution_methods, function(method) {
     # cibersort requires the binary path to be set, n/a in unittest.

diff --git a/tests/testthat/test_deconvolution_mouse.R b/tests/testthat/test_deconvolution_mouse.R
@@ -18,12 +18,12 @@ test_that("DCQ works", {
 })
 
 test_that("BASE works", {
-  res <- deconvolute_base_algorithm(test_mat)
+  res <- deconvolute_base_algorithm(test_mat, n_permutations = 5)
   assert("matrix dimensions consistent", ncol(res) == ncol(test_mat))
 })
 
 test_that("DCQ works without reducing cell types", {
-  res <- deconvolute_dcq(test_mat, combine_cells = FALSE)
+  res <- deconvolute_dcq(test_mat, combine_cells = FALSE, n_repeats = 5)
   assert("matrix dimensions consistent", ncol(res) == ncol(test_mat))
 })