| ... | ... |
@@ -1,6 +1,6 @@ |
| 1 | 1 |
Package: batchelor |
| 2 |
-Version: 1.6.1 |
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| 3 |
-Date: 2020-11-16 |
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| 2 |
+Version: 1.6.2 |
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| 3 |
+Date: 2020-11-25 |
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| 4 | 4 |
Title: Single-Cell Batch Correction Methods |
| 5 | 5 |
Authors@R: c(person("Aaron", "Lun", role = c("aut", "cre"), email = "infinite.monkeys.with.keyboards@gmail.com"),
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| 6 | 6 |
person("Laleh", "Haghverdi", role="ctb"))
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| ... | ... |
@@ -39,11 +39,7 @@ |
| 39 | 39 |
#' @export |
| 40 | 40 |
#' @importMethodsFrom BiocGenerics nrow ncol |
| 41 | 41 |
#' @importFrom BiocGenerics colnames rownames |
| 42 |
-checkBatchConsistency <- function(batches, cells.in.columns=TRUE) |
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| 43 |
-# Checking for identical number of rows (and rownames). |
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| 44 |
-# It can also do the same for columns, if we're dealing with PC results. |
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| 45 |
-# It then returns a list of dimnames for renaming the output. |
|
| 46 |
-{
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|
| 42 |
+checkBatchConsistency <- function(batches, cells.in.columns=TRUE) {
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|
| 47 | 43 |
if (length(batches)==0L) {
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| 48 | 44 |
return(invisible(NULL)) |
| 49 | 45 |
} |
| ... | ... |
@@ -65,18 +61,28 @@ checkBatchConsistency <- function(batches, cells.in.columns=TRUE) |
| 65 | 61 |
for (b in seq_along(batches)[-1]) {
|
| 66 | 62 |
current <- batches[[b]] |
| 67 | 63 |
if (!identical(DIMFUN(current), ref.n)) {
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| 68 |
- stop(sprintf("number of %ss is not the same across batches", DIM))
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|
| 64 |
+ stop(sprintf("number of %ss is not the same across batches (see batch %s)",
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| 65 |
+ DIM, .identify_failed_batch(b, names(batches)))) |
|
| 69 | 66 |
} |
| 70 | 67 |
|
| 71 | 68 |
cur.names <- DIMNAMEFUN(current) |
| 72 | 69 |
if (!identical(cur.names, ref.names)) {
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| 73 |
- stop(sprintf("%s names are not the same across batches", DIM))
|
|
| 70 |
+ stop(sprintf("%s names are not the same across batches (see batch %s)",
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|
| 71 |
+ DIM, .identify_failed_batch(b, names(batches)))) |
|
| 74 | 72 |
} |
| 75 | 73 |
} |
| 76 | 74 |
|
| 77 | 75 |
invisible(NULL) |
| 78 | 76 |
} |
| 79 | 77 |
|
| 78 |
+.identify_failed_batch <- function(bx, names) {
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| 79 |
+ if (is.null(names) || names[bx]=="") {
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| 80 |
+ bx |
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| 81 |
+ } else {
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| 82 |
+ deparse(names[bx]) |
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| 83 |
+ } |
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| 84 |
+} |
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| 85 |
+ |
|
| 80 | 86 |
#' @rdname checkInputs |
| 81 | 87 |
#' @export |
| 82 | 88 |
#' @importFrom methods is |
| ... | ... |
@@ -50,6 +50,17 @@ test_that("checkBatchConsistency handles corner cases", {
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| 50 | 50 |
expect_error(checkBatchConsistency(list(B[,0], B[,0]), cells.in.columns=FALSE), NA) |
| 51 | 51 |
}) |
| 52 | 52 |
|
| 53 |
+set.seed(10000012) |
|
| 54 |
+test_that("checkBatchConsistency reports names correctly", {
|
|
| 55 |
+ expect_error(checkBatchConsistency(list(cbind(1), cbind(1:2))), "batch 2") |
|
| 56 |
+ expect_error(checkBatchConsistency(list(cbind(1), X=cbind(1:2))), "batch \"X\"") |
|
| 57 |
+ expect_error(checkBatchConsistency(list(X=cbind(1), cbind(1:2))), "batch 2") |
|
| 58 |
+ |
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| 59 |
+ expect_error(checkBatchConsistency(list(rbind(A=1), rbind(B=2))), "batch 2") |
|
| 60 |
+ expect_error(checkBatchConsistency(list(rbind(A=1), X=rbind(B=2))), "batch \"X\"") |
|
| 61 |
+ expect_error(checkBatchConsistency(list(X=rbind(A=1), rbind(B=2))), "batch 2") |
|
| 62 |
+}) |
|
| 63 |
+ |
|
| 53 | 64 |
set.seed(1000003) |
| 54 | 65 |
test_that("checkIfSCE works correctly", {
|
| 55 | 66 |
sce1 <- SingleCellExperiment(list(logcounts=matrix(runif(5000), nrow=10))) |
