fix: streamline Heatmap feature logs

NEWS.md

@@ -9,3 +9,4 @@
 * Add `sample.name.column` to select the metadata column used for sample filtering, defaulting to `orig.ident` (#100).
 * Log requested sample filtering and displayed filtered/total cell counts (#101).
 * Use all samples when sample selection is blank (#102).
+* Report found Heatmap features before missing requested features without duplicate warnings (#103).

R/Heatmap.R

@@ -292,20 +292,19 @@ heatmapSC <- function(object,
   }
   transcript.data <- object@assays[[use.assay]]@scale.data
   missing.genes <- setdiff(transcripts, rownames(transcript.data))
+  transcripts <- transcripts[transcripts %in% rownames(transcript.data)]
+  if (length(transcripts) > 0) {
+    message("Transcripts found in ", use.assay, ": ",
+            paste(transcripts, collapse = ", "))
+  }
   if (length(missing.genes) > 0) {
     missing.transcript.message <- paste0(
       "There are ", length(missing.genes), " gene(s) absent from dataset: ",
       paste(shQuote(missing.genes), collapse = ", "),
-      ". Possible reasons are that gene is not official gene symbol or gene is ",
-      "not highly expressed and has been filtered."
+      ".\n          Possible reasons are that gene is not official gene symbol ",
+      "or gene is not highly expressed and has been filtered."
     )
     message(missing.transcript.message)
-    warning(missing.transcript.message)
-  }
-  transcripts <- transcripts[transcripts %in% rownames(transcript.data)]
-  if (length(transcripts) > 0) {
-    message("Transcripts found in ", use.assay, ": ",
-            paste(transcripts, collapse = ", "))
   }
 
   if (length(proteins) > 0 && !"Protein" %in% names(object@assays)) {
@@ -314,18 +313,17 @@ heatmapSC <- function(object,
 
   if (length(proteins) > 0) {
     missing.proteins <- setdiff(proteins, rownames(object$Protein@scale.data))
+    proteins <- proteins[proteins %in% rownames(object$Protein@scale.data)]
+    if (length(proteins) > 0) {
+      message("Proteins found in Protein assay: ",
+              paste(proteins, collapse = ", "))
+    }
     if (length(missing.proteins) > 0) {
       missing.protein.message <- paste0(
         "Proteins not found in Protein assay: ",
         paste(missing.proteins, collapse = ", "), ". They will be excluded."
       )
       message(missing.protein.message)
-      warning(missing.protein.message)
-    }
-    proteins <- proteins[proteins %in% rownames(object$Protein@scale.data)]
-    if (length(proteins) > 0) {
-      message("Proteins found in Protein assay: ",
-              paste(proteins, collapse = ", "))
     }
   }
 

tests/testthat/test-Heatmap.R

@@ -192,19 +192,22 @@ test_that("Heatmap run with bad gene name", {
   #Spike in with bad gene name
   cr.object$transcripts <- c("badgene", cr.object$transcripts)
   missing.transcript.message <- paste0(
-    "There are 1 gene(s) absent from dataset: 'badgene'. Possible reasons are ",
-    "that gene is not official gene symbol or gene is not highly expressed and ",
-    "has been filtered."
+    "There are 1 gene(s) absent from dataset: 'badgene'.\n",
+    "          Possible reasons are that gene is not official gene symbol or gene ",
+    "is not highly expressed and has been filtered."
   )
 
-  expect_warning(
-    expect_message(
+  expect_no_warning(
+    logs <- capture.output(
       do.call(heatmapSC, cr.object),
-      missing.transcript.message,
-      fixed = TRUE
-    ),
-    missing.transcript.message,
-    fixed = TRUE
+      type = "message"
+    )
+  )
+  log.text <- paste(logs, collapse = "\n")
+  expect_true(grepl(missing.transcript.message, log.text, fixed = TRUE))
+  expect_lt(
+    grep("Transcripts found in", logs, fixed = TRUE)[[1]],
+    grep("There are 1 gene(s) absent from dataset", logs, fixed = TRUE)[[1]]
   )
 })
 
@@ -213,12 +216,18 @@ test_that("Heatmap reports missing proteins and retains available proteins", {
   cr.object$proteins <- c("CD3", "not_a_protein")
   cr.object$protein.annotations <- NULL
 
-  expect_warning(
-    expect_message(
+  expect_no_warning(
+    logs <- capture.output(
       output <- do.call(heatmapSC, cr.object),
-      "Proteins not found in Protein assay: not_a_protein. They will be excluded."
-    ),
+      type = "message"
+    )
+  )
+  missing.protein.message <-
     "Proteins not found in Protein assay: not_a_protein. They will be excluded."
+  expect_true(any(grepl(missing.protein.message, logs, fixed = TRUE)))
+  expect_lt(
+    grep("Proteins found in", logs, fixed = TRUE)[[1]],
+    grep(missing.protein.message, logs, fixed = TRUE)[[1]]
   )
 
   expect_true("CD3_Prot" %in% output$data$gene)
@@ -264,20 +273,18 @@ test_that("Heatmap run with error for missing all genes", {
     c("APOE", "ARG1", "CD38", "CD3D", "CD3E", "CD3G")
   missing.transcript.message <- paste0(
     "There are 6 gene(s) absent from dataset: 'APOE', 'ARG1', 'CD38', 'CD3D', ",
-    "'CD3E', 'CD3G'. Possible reasons are that gene is not official gene symbol ",
-    "or gene is not highly expressed and has been filtered."
+    "'CD3E', 'CD3G'.\n          Possible reasons are that gene is not official ",
+    "gene symbol or gene is not highly expressed and has been filtered."
   )
-  expect_warning(
+  expect_no_warning(
     expect_message(
       expect_error(
         do.call(heatmapSC, cr.object),
         "No requested transcripts or proteins were found in the selected assays."
       ),
       missing.transcript.message,
       fixed = TRUE
-    ),
-    missing.transcript.message,
-    fixed = TRUE
+    )
   )
 
 })