From e9b9e752d4e994b19362a5f004b4dbf07361b44c Mon Sep 17 00:00:00 2001 From: LTLA Date: Tue, 15 Oct 2024 00:00:21 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20kanavers?= =?UTF-8?q?e/scran.js@e855f6bbdbd8e3578d907057be7e0d8b4003698b=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/AggregateAcrossCellsResults.html | 4 +- docs/BuildNeighborSearchIndexResults.html | 4 +- docs/BuildSnnGraphResults.html | 4 +- docs/ClusterKmeansResults.html | 4 +- docs/ClusterLeidenResults.html | 4 +- docs/ClusterMultilevelResults.html | 4 +- docs/ClusterWalktrapResults.html | 4 +- docs/FindNearestNeighborsResults.html | 115 +++++++++++++++++- docs/H5Base.html | 4 +- docs/H5DataSet.html | 4 +- docs/H5File.html | 4 +- docs/H5Group.html | 4 +- docs/IntegrateLabelCellsResults.html | 4 +- docs/IntegratedLabelCellsReferences.html | 4 +- docs/LabelCellsResults.html | 4 +- docs/LoadedLabelCellsReference.html | 4 +- docs/ModelGeneVariancesResults.html | 4 +- docs/MultiMatrix.html | 4 +- docs/MultiMatrix.js.html | 4 +- docs/PerCellAdtQcMetricsResults.html | 4 +- docs/PerCellCrisprQcMetricsResults.html | 4 +- docs/PerCellRnaQcMetricsResults.html | 4 +- docs/RdsBooleanVector.html | 4 +- docs/RdsDetails.html | 4 +- docs/RdsDoubleVector.html | 4 +- docs/RdsGenericVector.html | 4 +- docs/RdsIntegerVector.html | 4 +- docs/RdsNull.html | 4 +- docs/RdsObject.html | 4 +- docs/RdsS4Object.html | 4 +- docs/RdsStringVector.html | 4 +- docs/RdsVector.html | 4 +- docs/RunPcaResults.html | 4 +- docs/ScoreMarkersResults.html | 4 +- docs/ScranMatrix.html | 4 +- docs/ScranMatrix.js.html | 4 +- docs/SuggestAdtQcFiltersResults.html | 4 +- docs/SuggestCrisprQcFiltersResults.html | 4 +- docs/SuggestRnaQcFiltersResults.html | 4 +- docs/TrainedLabelCellsReference.html | 4 +- docs/TsneStatus.html | 4 +- docs/UmapStatus.html | 4 +- docs/aggregateAcrossCells.js.html | 4 +- docs/block.js.html | 4 +- docs/buildSnnGraph.js.html | 17 ++- docs/cbind.js.html | 4 +- docs/chooseHvgs.js.html | 4 +- docs/clusterGraph.js.html | 4 +- docs/clusterKmeans.js.html | 4 +- docs/computeClrm1Factors.js.html | 4 +- docs/delayed.js.html | 4 +- docs/factorize.js.html | 4 +- docs/file.js.html | 4 +- docs/filterCells.js.html | 4 +- docs/findNearestNeighbors.js.html | 13 +- docs/global.html | 72 ++++++----- docs/guessFeatures.js.html | 4 +- docs/hdf5.js.html | 4 +- docs/hypergeometricTest.js.html | 4 +- docs/index.html | 4 +- docs/initializeSparseMatrixFromArrays.js.html | 4 +- docs/initializeSparseMatrixFromHdf5.js.html | 4 +- ...ializeSparseMatrixFromMatrixMarket.js.html | 4 +- docs/initializeSparseMatrixFromRds.js.html | 4 +- docs/labelCells.js.html | 4 +- docs/mnnCorrect.js.html | 4 +- docs/modelGeneVariances.js.html | 4 +- docs/normalizeCounts.js.html | 4 +- docs/perCellAdtQcMetrics.js.html | 4 +- docs/perCellCrisprQcMetrics.js.html | 4 +- docs/perCellRnaQcMetrics.js.html | 4 +- docs/rds.js.html | 4 +- docs/realizeFile.js.html | 4 +- docs/runPca.js.html | 4 +- docs/runTsne.js.html | 61 +++++----- docs/runUmap.js.html | 29 +++-- docs/scaleByNeighbors.js.html | 4 +- docs/scoreGsdecon.js.html | 4 +- docs/scoreMarkers.js.html | 4 +- docs/subset.js.html | 4 +- docs/suggestAdtQcFilters.js.html | 4 +- docs/suggestCrisprQcFilters.js.html | 4 +- docs/suggestRnaQcFilters.js.html | 4 +- docs/testGeneSetEnrichment.js.html | 4 +- docs/utils.js.html | 4 +- docs/wasm.js.html | 4 +- docs/writeSparseMatrixToHdf5.js.html | 4 +- 87 files changed, 382 insertions(+), 249 deletions(-) diff --git a/docs/AggregateAcrossCellsResults.html b/docs/AggregateAcrossCellsResults.html index 7ce28426..43489cac 100644 --- a/docs/AggregateAcrossCellsResults.html +++ b/docs/AggregateAcrossCellsResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1525,7 +1525,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/BuildNeighborSearchIndexResults.html b/docs/BuildNeighborSearchIndexResults.html index 53cdacda..257d89f9 100644 --- a/docs/BuildNeighborSearchIndexResults.html +++ b/docs/BuildNeighborSearchIndexResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -406,7 +406,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/BuildSnnGraphResults.html b/docs/BuildSnnGraphResults.html index 6a3939d7..8d0ee43f 100644 --- a/docs/BuildSnnGraphResults.html +++ b/docs/BuildSnnGraphResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -196,7 +196,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/ClusterKmeansResults.html b/docs/ClusterKmeansResults.html index 6d157663..8adf171c 100644 --- a/docs/ClusterKmeansResults.html +++ b/docs/ClusterKmeansResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1364,7 +1364,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/ClusterLeidenResults.html b/docs/ClusterLeidenResults.html index ab94fe33..59db8396 100644 --- a/docs/ClusterLeidenResults.html +++ b/docs/ClusterLeidenResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -552,7 +552,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/ClusterMultilevelResults.html b/docs/ClusterMultilevelResults.html index e3d04201..7803370f 100644 --- a/docs/ClusterMultilevelResults.html +++ b/docs/ClusterMultilevelResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -940,7 +940,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/ClusterWalktrapResults.html b/docs/ClusterWalktrapResults.html index 1c9af7d1..f6f83f0e 100644 --- a/docs/ClusterWalktrapResults.html +++ b/docs/ClusterWalktrapResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -797,7 +797,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/FindNearestNeighborsResults.html b/docs/FindNearestNeighborsResults.html index 4c1e3da3..c4a89169 100644 --- a/docs/FindNearestNeighborsResults.html +++ b/docs/FindNearestNeighborsResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -99,7 +99,7 @@

(static)
Source:
@@ -320,7 +320,7 @@

freeSource:
@@ -507,6 +507,111 @@
Returns:
+

numberOfNeighbors() → {number}

+ + + + + + +
+ + +
Source:
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Returns:
+ + +
+

Number of neighbors that were requested in the search.

+
+ + + +
+
+ Type +
+
+ +number + + +
+
+ + + + + + + + + +

serialize(optionsopt) → {object}

@@ -519,7 +624,7 @@

serializeSource:
@@ -1144,7 +1249,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/H5Base.html b/docs/H5Base.html index 520a8f49..904238a3 100644 --- a/docs/H5Base.html +++ b/docs/H5Base.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1076,7 +1076,7 @@
Properties

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/H5DataSet.html b/docs/H5DataSet.html index 59a82ff7..619482d2 100644 --- a/docs/H5DataSet.html +++ b/docs/H5DataSet.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -2011,7 +2011,7 @@
Properties

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/H5File.html b/docs/H5File.html index ec09c41b..9fccbaf8 100644 --- a/docs/H5File.html +++ b/docs/H5File.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -2607,7 +2607,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/H5Group.html b/docs/H5Group.html index 9542ce6e..e8ca0f5c 100644 --- a/docs/H5Group.html +++ b/docs/H5Group.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -2617,7 +2617,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/IntegrateLabelCellsResults.html b/docs/IntegrateLabelCellsResults.html index 488d2de2..5acb1e0e 100644 --- a/docs/IntegrateLabelCellsResults.html +++ b/docs/IntegrateLabelCellsResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1508,7 +1508,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/IntegratedLabelCellsReferences.html b/docs/IntegratedLabelCellsReferences.html index 44bb31d4..cba1583f 100644 --- a/docs/IntegratedLabelCellsReferences.html +++ b/docs/IntegratedLabelCellsReferences.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -294,7 +294,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/LabelCellsResults.html b/docs/LabelCellsResults.html index ba9d796f..94a46e76 100644 --- a/docs/LabelCellsResults.html +++ b/docs/LabelCellsResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1509,7 +1509,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/LoadedLabelCellsReference.html b/docs/LoadedLabelCellsReference.html index e6d7797f..2d16fa3f 100644 --- a/docs/LoadedLabelCellsReference.html +++ b/docs/LoadedLabelCellsReference.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -504,7 +504,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/ModelGeneVariancesResults.html b/docs/ModelGeneVariancesResults.html index a88f5081..daee9dfa 100644 --- a/docs/ModelGeneVariancesResults.html +++ b/docs/ModelGeneVariancesResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1574,7 +1574,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/MultiMatrix.html b/docs/MultiMatrix.html index b3ab2a07..1ea30ca9 100644 --- a/docs/MultiMatrix.html +++ b/docs/MultiMatrix.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1570,7 +1570,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/MultiMatrix.js.html b/docs/MultiMatrix.js.html index bad51925..91822822 100644 --- a/docs/MultiMatrix.js.html +++ b/docs/MultiMatrix.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -199,7 +199,7 @@

MultiMatrix.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/PerCellAdtQcMetricsResults.html b/docs/PerCellAdtQcMetricsResults.html index 6de9c38e..fa264224 100644 --- a/docs/PerCellAdtQcMetricsResults.html +++ b/docs/PerCellAdtQcMetricsResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1179,7 +1179,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/PerCellCrisprQcMetricsResults.html b/docs/PerCellCrisprQcMetricsResults.html index 44b3ac6b..e753bdb6 100644 --- a/docs/PerCellCrisprQcMetricsResults.html +++ b/docs/PerCellCrisprQcMetricsResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1390,7 +1390,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/PerCellRnaQcMetricsResults.html b/docs/PerCellRnaQcMetricsResults.html index da2519cd..98176b11 100644 --- a/docs/PerCellRnaQcMetricsResults.html +++ b/docs/PerCellRnaQcMetricsResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1179,7 +1179,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RdsBooleanVector.html b/docs/RdsBooleanVector.html index e1b1e4e5..dfc55448 100644 --- a/docs/RdsBooleanVector.html +++ b/docs/RdsBooleanVector.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1085,7 +1085,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RdsDetails.html b/docs/RdsDetails.html index 6da4de09..512eda98 100644 --- a/docs/RdsDetails.html +++ b/docs/RdsDetails.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -612,7 +612,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RdsDoubleVector.html b/docs/RdsDoubleVector.html index db1433ab..58a10a73 100644 --- a/docs/RdsDoubleVector.html +++ b/docs/RdsDoubleVector.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1084,7 +1084,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RdsGenericVector.html b/docs/RdsGenericVector.html index c303fecf..15b41e8b 100644 --- a/docs/RdsGenericVector.html +++ b/docs/RdsGenericVector.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -989,7 +989,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RdsIntegerVector.html b/docs/RdsIntegerVector.html index 5d9432c3..169a031b 100644 --- a/docs/RdsIntegerVector.html +++ b/docs/RdsIntegerVector.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1084,7 +1084,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RdsNull.html b/docs/RdsNull.html index d91474a9..98fe5d5c 100644 --- a/docs/RdsNull.html +++ b/docs/RdsNull.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -315,7 +315,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RdsObject.html b/docs/RdsObject.html index 60dc3e25..0295690a 100644 --- a/docs/RdsObject.html +++ b/docs/RdsObject.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -294,7 +294,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RdsS4Object.html b/docs/RdsS4Object.html index 56edb5d4..db250ea2 100644 --- a/docs/RdsS4Object.html +++ b/docs/RdsS4Object.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -906,7 +906,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RdsStringVector.html b/docs/RdsStringVector.html index ac56db42..204f0f5e 100644 --- a/docs/RdsStringVector.html +++ b/docs/RdsStringVector.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -940,7 +940,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RdsVector.html b/docs/RdsVector.html index 958a946b..b3ab2b8f 100644 --- a/docs/RdsVector.html +++ b/docs/RdsVector.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -815,7 +815,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/RunPcaResults.html b/docs/RunPcaResults.html index fef16342..f02b5982 100644 --- a/docs/RunPcaResults.html +++ b/docs/RunPcaResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1252,7 +1252,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/ScoreMarkersResults.html b/docs/ScoreMarkersResults.html index fd3f7ef7..95d67dee 100644 --- a/docs/ScoreMarkersResults.html +++ b/docs/ScoreMarkersResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -2169,7 +2169,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/ScranMatrix.html b/docs/ScranMatrix.html index 6f23429c..3bc1293c 100644 --- a/docs/ScranMatrix.html +++ b/docs/ScranMatrix.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1263,7 +1263,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/ScranMatrix.js.html b/docs/ScranMatrix.js.html index 52628fd8..726764af 100644 --- a/docs/ScranMatrix.js.html +++ b/docs/ScranMatrix.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -187,7 +187,7 @@

ScranMatrix.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/SuggestAdtQcFiltersResults.html b/docs/SuggestAdtQcFiltersResults.html index ea06d194..5296482b 100644 --- a/docs/SuggestAdtQcFiltersResults.html +++ b/docs/SuggestAdtQcFiltersResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1415,7 +1415,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/SuggestCrisprQcFiltersResults.html b/docs/SuggestCrisprQcFiltersResults.html index 0cc604fd..80103645 100644 --- a/docs/SuggestCrisprQcFiltersResults.html +++ b/docs/SuggestCrisprQcFiltersResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -923,7 +923,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/SuggestRnaQcFiltersResults.html b/docs/SuggestRnaQcFiltersResults.html index 5ff297a3..9088370e 100644 --- a/docs/SuggestRnaQcFiltersResults.html +++ b/docs/SuggestRnaQcFiltersResults.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -1661,7 +1661,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/TrainedLabelCellsReference.html b/docs/TrainedLabelCellsReference.html index de749ce4..61e887e6 100644 --- a/docs/TrainedLabelCellsReference.html +++ b/docs/TrainedLabelCellsReference.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -399,7 +399,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/TsneStatus.html b/docs/TsneStatus.html index d7d35dd5..df17aa16 100644 --- a/docs/TsneStatus.html +++ b/docs/TsneStatus.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -900,7 +900,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/UmapStatus.html b/docs/UmapStatus.html index a9cadeda..766cff39 100644 --- a/docs/UmapStatus.html +++ b/docs/UmapStatus.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -964,7 +964,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/aggregateAcrossCells.js.html b/docs/aggregateAcrossCells.js.html index 64b9b6fb..98088140 100644 --- a/docs/aggregateAcrossCells.js.html +++ b/docs/aggregateAcrossCells.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -240,7 +240,7 @@

aggregateAcrossCells.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/block.js.html b/docs/block.js.html index f9d9c5d3..07f377b2 100644 --- a/docs/block.js.html +++ b/docs/block.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -110,7 +110,7 @@

block.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/buildSnnGraph.js.html b/docs/buildSnnGraph.js.html index 19eeedbd..4bb04de5 100644 --- a/docs/buildSnnGraph.js.html +++ b/docs/buildSnnGraph.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -81,11 +81,13 @@

buildSnnGraph.js

} /** - * Build a shared nearest graph. + * Build a shared nearest graph where each cell is a node. + * Edges are formed between cells that share one or more nearest neighbors, weighted by the number or rank of those shared neighbors. * - * @param {BuildNeighborSearchIndexResults|FindNearestNeighborsResults} x - * Either a pre-built neighbor search index for the dataset (see {@linkcode buildNeighborSearchIndex}), - * or a pre-computed set of neighbor search results for all cells (see {@linkcode findNearestNeighbors}). + * @param {BuildNeighborSearchIndexResults|FindNearestNeighborsResults} x A pre-built neighbor search index from {@linkcode buildNeighborSearchIndex}. + * + * Alternatively, a pre-computed set of neighbor search results from {linkcode findNearestNeighbors}. + * The number of neighbors should be equal to `neighbors`, otherwise a warning is raised. * @param {object} [options={}] - Optional parameters. * @param {number} [options.scheme="rank"] - Weighting scheme for the edges between cells. * This can be based on the top ranks of the shared neighbors (`"rank"`), @@ -110,6 +112,9 @@

buildSnnGraph.js

try { let ref; if (x instanceof FindNearestNeighborsResults) { + if (neighbors != x.numberOfNeighbors()) { + console.warn("number of neighbors in 'x' does not match 'neighbors'"); + } ref = x; } else { my_neighbors = findNearestNeighbors(x, neighbors, { numberOfThreads: nthreads }); @@ -146,7 +151,7 @@

buildSnnGraph.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/cbind.js.html b/docs/cbind.js.html index 65106585..76ff4627 100644 --- a/docs/cbind.js.html +++ b/docs/cbind.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -221,7 +221,7 @@

cbind.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/chooseHvgs.js.html b/docs/chooseHvgs.js.html index 5806f847..2058f9ac 100644 --- a/docs/chooseHvgs.js.html +++ b/docs/chooseHvgs.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -110,7 +110,7 @@

chooseHvgs.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/clusterGraph.js.html b/docs/clusterGraph.js.html index d3a3b330..14901882 100644 --- a/docs/clusterGraph.js.html +++ b/docs/clusterGraph.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -301,7 +301,7 @@

clusterGraph.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/clusterKmeans.js.html b/docs/clusterKmeans.js.html index 88a8f001..b4b138e0 100644 --- a/docs/clusterKmeans.js.html +++ b/docs/clusterKmeans.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -251,7 +251,7 @@

clusterKmeans.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/computeClrm1Factors.js.html b/docs/computeClrm1Factors.js.html index 017a336b..971c14d8 100644 --- a/docs/computeClrm1Factors.js.html +++ b/docs/computeClrm1Factors.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -100,7 +100,7 @@

computeClrm1Factors.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/delayed.js.html b/docs/delayed.js.html index 40daf00b..a15b9f27 100644 --- a/docs/delayed.js.html +++ b/docs/delayed.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -189,7 +189,7 @@

delayed.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/factorize.js.html b/docs/factorize.js.html index 95982fb8..492ce1a9 100644 --- a/docs/factorize.js.html +++ b/docs/factorize.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -358,7 +358,7 @@

factorize.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/file.js.html b/docs/file.js.html index 01b02b65..e9b17fe0 100644 --- a/docs/file.js.html +++ b/docs/file.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -109,7 +109,7 @@

file.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/filterCells.js.html b/docs/filterCells.js.html index 1933cce1..8a2edbae 100644 --- a/docs/filterCells.js.html +++ b/docs/filterCells.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -78,7 +78,7 @@

filterCells.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/findNearestNeighbors.js.html b/docs/findNearestNeighbors.js.html index 3f8a8fd0..d094a17f 100644 --- a/docs/findNearestNeighbors.js.html +++ b/docs/findNearestNeighbors.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -160,7 +160,7 @@

findNearestNeighbors.js

export class FindNearestNeighborsResults { #id; #results; - +u constructor(id, raw) { this.#id = id; this.#results = raw; @@ -187,6 +187,13 @@

findNearestNeighbors.js

return this.#results.num_obs(); } + /** + * @return {number} Number of neighbors that were requested in the search. + */ + numberOfNeighbors() { + return this.#results.num_neighbors(); + } + // Internal use only, not documented. get results() { return this.#results; @@ -365,7 +372,7 @@

findNearestNeighbors.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/global.html b/docs/global.html index 99ed1704..72e9538a 100644 --- a/docs/global.html +++ b/docs/global.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -879,7 +879,7 @@

buildSnn
Source:
@@ -919,7 +919,8 @@

buildSnn
-

Build a shared nearest graph.

+

Build a shared nearest graph where each cell is a node. +Edges are formed between cells that share one or more nearest neighbors, weighted by the number or rank of those shared neighbors.

@@ -992,8 +993,9 @@

Parameters:
-

Either a pre-built neighbor search index for the dataset (see buildNeighborSearchIndex), -or a pre-computed set of neighbor search results for all cells (see findNearestNeighbors).

+

A pre-built neighbor search index from buildNeighborSearchIndex.

+

Alternatively, a pre-computed set of neighbor search results from {linkcode findNearestNeighbors}. +The number of neighbors should be equal to neighbors, otherwise a warning is raised.

@@ -8486,7 +8488,7 @@

f
Source:
@@ -13755,7 +13757,7 @@

initial
Source:
@@ -13864,8 +13866,9 @@

Parameters:
-

Either a pre-built neighbor search index for the dataset (see buildNeighborSearchIndex), -or a pre-computed set of neighbor search results for all cells (see findNearestNeighbors).

+

A pre-built neighbor search index from buildNeighborSearchIndex.

+

Alternatively, a pre-computed set of neighbor search results from {linkcode findNearestNeighbors}. +The number of neighbors should be equal to neighbors, otherwise a warning is raised.

@@ -13973,13 +13976,13 @@
Properties
- checkMismatch + neighbors -boolean +number @@ -13992,6 +13995,8 @@
Properties
+ <nullable>
+ @@ -14000,13 +14005,13 @@
Properties
- true + null -

Whether to check for a mismatch between the perplexity and the number of searched neighbors. -Only relevant if x is a FindNearestNeighborsResults object.

+

Number of nearest neighbors to find. +If null, defaults to the output of perplexityToNeighbors(perplexity).

@@ -14119,7 +14124,7 @@

initial
Source:
@@ -14228,8 +14233,11 @@

Parameters:
-

Either a pre-built neighbor search index for the dataset (see buildNeighborSearchIndex), -or a pre-computed set of neighbor search results for all cells (see findNearestNeighbors).

+ +

Alternatively, a pre-computed set of neighbor search results for all cells (see findNearestNeighbors). +The number of neighbors should be equal to neighbors, otherwise a warning is raised.

@@ -21355,7 +21363,7 @@

runTsneSource:
@@ -21469,8 +21477,9 @@
Parameters:
-

Either a pre-built neighbor search index for the dataset (see buildNeighborSearchIndex), -or a pre-computed set of neighbor search results for all cells (see findNearestNeighbors).

+

A pre-built neighbor search index from buildNeighborSearchIndex.

+

Alternatively, a pre-computed set of neighbor search results from {linkcode findNearestNeighbors}. +The number of neighbors should be equal to neighbors, otherwise a warning is raised.

@@ -21578,13 +21587,13 @@
Properties
- checkMismatch + neighbors -boolean +number @@ -21597,6 +21606,8 @@
Properties
+ <nullable>
+ @@ -21605,13 +21616,13 @@
Properties
- true + null -

Whether to check for a mismatch between the perplexity and the number of searched neighbors. -Only relevant if x is a FindNearestNeighborsResults object.

+

Number of nearest neighbors to find. +If null, defaults to the output of perplexityToNeighbors(perplexity).

@@ -21763,7 +21774,7 @@

runUmapSource:
@@ -21877,8 +21888,9 @@
Parameters:
-

Either a pre-built neighbor search index for the dataset (see buildNeighborSearchIndex), -or a pre-computed set of neighbor search results for all cells (see findNearestNeighbors).

+

A pre-built neighbor search index from buildNeighborSearchIndex.

+

Alternatively, a pre-computed set of neighbor search results from {linkcode findNearestNeighbors}. +The number of neighbors should be equal to neighbors, otherwise a warning is raised.

@@ -27383,7 +27395,7 @@

Source:
@@ -28234,7 +28246,7 @@
Returns:

- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/guessFeatures.js.html b/docs/guessFeatures.js.html index 619d4254..386318b0 100644 --- a/docs/guessFeatures.js.html +++ b/docs/guessFeatures.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -256,7 +256,7 @@

guessFeatures.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/hdf5.js.html b/docs/hdf5.js.html index 72a41722..d92f6522 100644 --- a/docs/hdf5.js.html +++ b/docs/hdf5.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -860,7 +860,7 @@

hdf5.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/hypergeometricTest.js.html b/docs/hypergeometricTest.js.html index dd3227a1..f5fd801d 100644 --- a/docs/hypergeometricTest.js.html +++ b/docs/hypergeometricTest.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -165,7 +165,7 @@

hypergeometricTest.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/index.html b/docs/index.html index 66e71b8c..907ad3e9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -169,7 +169,7 @@

Links


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/initializeSparseMatrixFromArrays.js.html b/docs/initializeSparseMatrixFromArrays.js.html index f33f0a66..71085a32 100644 --- a/docs/initializeSparseMatrixFromArrays.js.html +++ b/docs/initializeSparseMatrixFromArrays.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -237,7 +237,7 @@

initializeSparseMatrixFromArrays.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/initializeSparseMatrixFromHdf5.js.html b/docs/initializeSparseMatrixFromHdf5.js.html index 8d0681c8..b24283a0 100644 --- a/docs/initializeSparseMatrixFromHdf5.js.html +++ b/docs/initializeSparseMatrixFromHdf5.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -280,7 +280,7 @@

initializeSparseMatrixFromHdf5.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/initializeSparseMatrixFromMatrixMarket.js.html b/docs/initializeSparseMatrixFromMatrixMarket.js.html index c8c9a01d..1515f245 100644 --- a/docs/initializeSparseMatrixFromMatrixMarket.js.html +++ b/docs/initializeSparseMatrixFromMatrixMarket.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -152,7 +152,7 @@

initializeSparseMatrixFromMatrixMarket.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/initializeSparseMatrixFromRds.js.html b/docs/initializeSparseMatrixFromRds.js.html index 75141851..067f5ce1 100644 --- a/docs/initializeSparseMatrixFromRds.js.html +++ b/docs/initializeSparseMatrixFromRds.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -95,7 +95,7 @@

initializeSparseMatrixFromRds.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/labelCells.js.html b/docs/labelCells.js.html index 8dfd5bf0..4cf5594e 100644 --- a/docs/labelCells.js.html +++ b/docs/labelCells.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -843,7 +843,7 @@

labelCells.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/mnnCorrect.js.html b/docs/mnnCorrect.js.html index 57d92df2..a61650f8 100644 --- a/docs/mnnCorrect.js.html +++ b/docs/mnnCorrect.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -172,7 +172,7 @@

mnnCorrect.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/modelGeneVariances.js.html b/docs/modelGeneVariances.js.html index 88f03bd4..f1986d89 100644 --- a/docs/modelGeneVariances.js.html +++ b/docs/modelGeneVariances.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -232,7 +232,7 @@

modelGeneVariances.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/normalizeCounts.js.html b/docs/normalizeCounts.js.html index 6fb5e797..37d38e07 100644 --- a/docs/normalizeCounts.js.html +++ b/docs/normalizeCounts.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -175,7 +175,7 @@

normalizeCounts.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/perCellAdtQcMetrics.js.html b/docs/perCellAdtQcMetrics.js.html index 262da1f9..5d016a6b 100644 --- a/docs/perCellAdtQcMetrics.js.html +++ b/docs/perCellAdtQcMetrics.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -174,7 +174,7 @@

perCellAdtQcMetrics.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/perCellCrisprQcMetrics.js.html b/docs/perCellCrisprQcMetrics.js.html index 0763ec04..5578862e 100644 --- a/docs/perCellCrisprQcMetrics.js.html +++ b/docs/perCellCrisprQcMetrics.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -173,7 +173,7 @@

perCellCrisprQcMetrics.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/perCellRnaQcMetrics.js.html b/docs/perCellRnaQcMetrics.js.html index f80a4c10..4ceee85d 100644 --- a/docs/perCellRnaQcMetrics.js.html +++ b/docs/perCellRnaQcMetrics.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -174,7 +174,7 @@

perCellRnaQcMetrics.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/rds.js.html b/docs/rds.js.html index 259d6f3b..68bc1ed9 100644 --- a/docs/rds.js.html +++ b/docs/rds.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -451,7 +451,7 @@

rds.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/realizeFile.js.html b/docs/realizeFile.js.html index d12aeab0..4226bb51 100644 --- a/docs/realizeFile.js.html +++ b/docs/realizeFile.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -108,7 +108,7 @@

realizeFile.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/runPca.js.html b/docs/runPca.js.html index 58b5074d..ae34f398 100644 --- a/docs/runPca.js.html +++ b/docs/runPca.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -257,7 +257,7 @@

runPca.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/runTsne.js.html b/docs/runTsne.js.html index 8598d359..ae508a08 100644 --- a/docs/runTsne.js.html +++ b/docs/runTsne.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -149,49 +149,47 @@

runTsne.js

} /** - * @param {BuildNeighborSearchIndexResults|FindNearestNeighborsResults} x - * Either a pre-built neighbor search index for the dataset (see {@linkcode buildNeighborSearchIndex}), - * or a pre-computed set of neighbor search results for all cells (see {@linkcode findNearestNeighbors}). + * @param {BuildNeighborSearchIndexResults|FindNearestNeighborsResults} x A pre-built neighbor search index from {@linkcode buildNeighborSearchIndex}. + * + * Alternatively, a pre-computed set of neighbor search results from {linkcode findNearestNeighbors}. + * The number of neighbors should be equal to `neighbors`, otherwise a warning is raised. * @param {object} [options={}] - Optional parameters. * @param {number} [options.perplexity=30] - Perplexity to use when computing neighbor probabilities in the t-SNE. - * @param {boolean} [options.checkMismatch=true] - Whether to check for a mismatch between the perplexity and the number of searched neighbors. - * Only relevant if `x` is a {@linkplain FindNearestNeighborsResults} object. + * @param {?number} [options.neighbors=null] - Number of nearest neighbors to find. + * If `null`, defaults to the output of {@linkcode perplexityToNeighbors perplexityToNeighbors(perplexity)}. * @param {?number} [options.numberOfThreads=null] - Number of threads to use. * If `null`, defaults to {@linkcode maximumThreads}. * * @return {TsneStatus} Object containing the initial status of the t-SNE algorithm. */ export function initializeTsne(x, options = {}) { - const { perplexity = 30, checkMismatch = true, numberOfThreads = null, ...others } = options; + const { perplexity = 30, neighbors = null, numberOfThreads = null, ...others } = options; utils.checkOtherOptions(others); - var my_neighbors; + var my_nnres; var raw_coords; var output; let nthreads = utils.chooseNumberOfThreads(numberOfThreads); + const k = (neighbors == null ? perplexityToNeighbors(perplexity) : neighbors); + try { - let neighbors; + let nnres; if (x instanceof BuildNeighborSearchIndexResults) { - let k = perplexityToNeighbors(perplexity); - my_neighbors = findNearestNeighbors(x, k, { numberOfThreads: nthreads }); - neighbors = my_neighbors; - + my_nnres = findNearestNeighbors(x, k, { numberOfThreads: nthreads }); + nnres = my_nnres } else { - if (checkMismatch) { - let k = perplexityToNeighbors(perplexity); - if (k * x.numberOfCells() != x.size()) { - throw new Error("number of neighbors in 'x' does not match '3 * perplexity'"); - } + if (k != x.numberOfNeighbors()) { + console.warn("number of neighbors in 'x' does not match 'neighbors'"); } - neighbors = x; + nnres = x; } - raw_coords = utils.createFloat64WasmArray(2 * neighbors.numberOfCells()); - wasm.call(module => module.randomize_tsne_start(neighbors.numberOfCells(), raw_coords.offset, 42)); + raw_coords = utils.createFloat64WasmArray(2 * nnres.numberOfCells()); + wasm.call(module => module.randomize_tsne_start(nnres.numberOfCells(), raw_coords.offset, 42)); output = gc.call( - module => module.initialize_tsne(neighbors.results, perplexity, nthreads), + module => module.initialize_tsne(nnres.results, perplexity, nthreads), TsneStatus, raw_coords ); @@ -202,7 +200,7 @@

runTsne.js

throw e; } finally { - utils.free(my_neighbors); + utils.free(my_nnres); } return output; @@ -212,13 +210,14 @@

runTsne.js

* Run the t-SNE algorithm to the specified number of iterations. * This is a wrapper around {@linkcode initializeTsne} and {@linkcode TsneStatus#run run}. * - * @param {BuildNeighborSearchIndexResults|FindNearestNeighborsResults} x - * Either a pre-built neighbor search index for the dataset (see {@linkcode buildNeighborSearchIndex}), - * or a pre-computed set of neighbor search results for all cells (see {@linkcode findNearestNeighbors}). + * @param {BuildNeighborSearchIndexResults|FindNearestNeighborsResults} x A pre-built neighbor search index from {@linkcode buildNeighborSearchIndex}. + * + * Alternatively, a pre-computed set of neighbor search results from {linkcode findNearestNeighbors}. + * The number of neighbors should be equal to `neighbors`, otherwise a warning is raised. * @param {object} [options={}] - Optional parameters. * @param {number} [options.perplexity=30] - Perplexity to use when computing neighbor probabilities in the t-SNE. - * @param {boolean} [options.checkMismatch=true] - Whether to check for a mismatch between the perplexity and the number of searched neighbors. - * Only relevant if `x` is a {@linkplain FindNearestNeighborsResults} object. + * @param {?number} [options.neighbors=null] - Number of nearest neighbors to find. + * If `null`, defaults to the output of {@linkcode perplexityToNeighbors perplexityToNeighbors(perplexity)}. * @param {?number} [options.numberOfThreads=null] - Number of threads to use. * If `null`, defaults to {@linkcode maximumThreads}. * @param {number} [options.maxIterations=1000] - Maximum number of iterations to perform. @@ -226,9 +225,9 @@

runTsne.js

* @return {object} Object containing coordinates of the t-SNE embedding, see {@linkcode TsneStatus#extractCoordinates TsneStatus.extractCoordinates} for more details. */ export function runTsne(x, options = {}) { - const { perplexity = 30, checkMismatch = true, numberOfThreads = null, maxIterations = 1000, ...others } = options; + const { perplexity = 30, neighbors = null, numberOfThreads = null, maxIterations = 1000, ...others } = options; utils.checkOtherOptions(others); - let tstat = initializeTsne(x, { perplexity, checkMismatch, numberOfThreads }); + let tstat = initializeTsne(x, { perplexity, neighbors, numberOfThreads }); tstat.run({ maxIterations }); return tstat.extractCoordinates(); } @@ -246,7 +245,7 @@

runTsne.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/runUmap.js.html b/docs/runUmap.js.html index 0c3e240f..c067dacf 100644 --- a/docs/runUmap.js.html +++ b/docs/runUmap.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -146,9 +146,10 @@

runUmap.js

} /** - * @param {(BuildNeighborSearchIndexResults|FindNearestNeighborsResults)} x - * Either a pre-built neighbor search index for the dataset (see {@linkcode buildNeighborSearchIndex}), - * or a pre-computed set of neighbor search results for all cells (see {@linkcode findNearestNeighbors}). + * @param {BuildNeighborSearchIndexResults|FindNearestNeighborsResults} x * A pre-built neighbor search index for the dataset (see {@linkcode buildNeighborSearchIndex}). + * + * Alternatively, a pre-computed set of neighbor search results for all cells (see {@linkcode findNearestNeighbors}). + * The number of neighbors should be equal to `neighbors`, otherwise a warning is raised. * @param {object} [options={}] - Optional parameters. * @param {number} [options.neighbors=15] - Number of neighbors to use in the UMAP algorithm. * Ignored if `x` is a {@linkplain FindNearestNeighborsResults} object. @@ -163,7 +164,7 @@

runUmap.js

const { neighbors = 15, epochs = 500, minDist = 0.01, numberOfThreads = null, ...others } = options; utils.checkOtherOptions(others); - var my_neighbors; + var my_nnres; var raw_coords; var output; let nthreads = utils.chooseNumberOfThreads(numberOfThreads); @@ -172,9 +173,12 @@

runUmap.js

let nnres; if (x instanceof BuildNeighborSearchIndexResults) { - my_neighbors = findNearestNeighbors(x, neighbors, { numberOfThreads: nthreads }); - nnres = my_neighbors; + my_nnres = findNearestNeighbors(x, neighbors, { numberOfThreads: nthreads }); + nnres = my_nnres; } else { + if (neighbors != x.numberOfNeighbors()) { + console.warn("number of neighbors in 'x' does not match 'neighbors'"); + } nnres = x; } @@ -191,7 +195,7 @@

runUmap.js

throw e; } finally { - utils.free(my_neighbors); + utils.free(my_nnres); } return output; @@ -201,9 +205,10 @@

runUmap.js

* Run the UMAP algorithm. * This is a wrapper around {@linkcode initializeUmap} and {@linkcode UmapStatus#run run}. * - * @param {(BuildNeighborSearchIndexResults|FindNearestNeighborsResults)} x - * Either a pre-built neighbor search index for the dataset (see {@linkcode buildNeighborSearchIndex}), - * or a pre-computed set of neighbor search results for all cells (see {@linkcode findNearestNeighbors}). + * @param {BuildNeighborSearchIndexResults|FindNearestNeighborsResults} x A pre-built neighbor search index from {@linkcode buildNeighborSearchIndex}. + * + * Alternatively, a pre-computed set of neighbor search results from {linkcode findNearestNeighbors}. + * The number of neighbors should be equal to `neighbors`, otherwise a warning is raised. * @param {object} [options={}] - Optional parameters. * @param {number} [options.neighbors=15] - Number of neighbors to use in the UMAP algorithm. * Ignored if `x` is a {@linkplain FindNearestNeighborsResults} object. @@ -235,7 +240,7 @@

runUmap.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/scaleByNeighbors.js.html b/docs/scaleByNeighbors.js.html index dad574de..109a2c9b 100644 --- a/docs/scaleByNeighbors.js.html +++ b/docs/scaleByNeighbors.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -191,7 +191,7 @@

scaleByNeighbors.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/scoreGsdecon.js.html b/docs/scoreGsdecon.js.html index 25020f58..8c37a319 100644 --- a/docs/scoreGsdecon.js.html +++ b/docs/scoreGsdecon.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -133,7 +133,7 @@

scoreGsdecon.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/scoreMarkers.js.html b/docs/scoreMarkers.js.html index 0938707a..deebc2a1 100644 --- a/docs/scoreMarkers.js.html +++ b/docs/scoreMarkers.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -284,7 +284,7 @@

scoreMarkers.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/subset.js.html b/docs/subset.js.html index f82e7d5d..b59997f1 100644 --- a/docs/subset.js.html +++ b/docs/subset.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -217,7 +217,7 @@

subset.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/suggestAdtQcFilters.js.html b/docs/suggestAdtQcFilters.js.html index ebc90b59..ffa92103 100644 --- a/docs/suggestAdtQcFilters.js.html +++ b/docs/suggestAdtQcFilters.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -210,7 +210,7 @@

suggestAdtQcFilters.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/suggestCrisprQcFilters.js.html b/docs/suggestCrisprQcFilters.js.html index 611d0b18..39438788 100644 --- a/docs/suggestCrisprQcFilters.js.html +++ b/docs/suggestCrisprQcFilters.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -180,7 +180,7 @@

suggestCrisprQcFilters.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/suggestRnaQcFilters.js.html b/docs/suggestRnaQcFilters.js.html index 0c5c4599..f79846a2 100644 --- a/docs/suggestRnaQcFilters.js.html +++ b/docs/suggestRnaQcFilters.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -219,7 +219,7 @@

suggestRnaQcFilters.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/testGeneSetEnrichment.js.html b/docs/testGeneSetEnrichment.js.html index ffe44da7..5b8540ea 100644 --- a/docs/testGeneSetEnrichment.js.html +++ b/docs/testGeneSetEnrichment.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -202,7 +202,7 @@

testGeneSetEnrichment.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/utils.js.html b/docs/utils.js.html index 206cdb74..ec980961 100644 --- a/docs/utils.js.html +++ b/docs/utils.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -243,7 +243,7 @@

utils.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/wasm.js.html b/docs/wasm.js.html index 97e54dc5..afa4b787 100644 --- a/docs/wasm.js.html +++ b/docs/wasm.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -155,7 +155,7 @@

wasm.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.
diff --git a/docs/writeSparseMatrixToHdf5.js.html b/docs/writeSparseMatrixToHdf5.js.html index e80302fd..2fbf469f 100644 --- a/docs/writeSparseMatrixToHdf5.js.html +++ b/docs/writeSparseMatrixToHdf5.js.html @@ -29,7 +29,7 @@ -

Home

Github repo

Classes

Global

+

Home

Github repo

Classes

Global

@@ -106,7 +106,7 @@

writeSparseMatrixToHdf5.js


- Documentation generated by JSDoc 3.6.11 on Mon Oct 14 2024 22:23:22 GMT+0000 (Coordinated Universal Time) using the docdash theme. + Documentation generated by JSDoc 3.6.11 on Tue Oct 15 2024 00:00:20 GMT+0000 (Coordinated Universal Time) using the docdash theme.