Seurat v3.1.3 #2605
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Seurat v3.1.3 #2605
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Make AverageExpression faster by using the rowMeans functions, instead of apply. In addition it will now avoid making sparse matrices dense. Additionally add a test for AverageExpression.
Use rowMeans instead of apply in FindMarkers. This avoids making dense matrices of sparse matrices and is also faster.
Export DiscretePalette Minor style fixes
Don't materialize dense matrix in AverageExpression and FindMarkers
Use palettes from pals package
* preprocessing code to leiden algorithm input was changed between v3.1.1 and v3.1.2 producing different default behavior of FindCluster * this is to make it consistent to the previous version.
Switch back to previous default color scheme
Addresses satijala/seurat#2464
The `getEdges` method was a public method of the `Network` class that allows users to obtain a copy of the Edges of a Network object. This method/interface was ported over from Java to C++ with a bug in it, though because the `getEdges` method is never called by either the Java or C++ version of the code, this bug had no effect on the current code. However, to improve the code and maintain it's similarity with the original Java version, it's probably worth fixing this unused method. The specific bug was that instead of filling an array from `start + value_1` to `start + value_2` with a constant value, it was filled from `start + value_1` to `end + value_2` with a constant value, which leads to unexpected behavior due to an array overflow.
Fix getEdges() Method of the Network Class
Addresses #2466. uwot throws the error: "Sparse matrices are only supported as distance matrices" when given a feature matrix. This coerces to a dense matrix to handle that case.
Enable uwot on feature matrix
When a key name with an underscore in the middle is passed to functions that generate DimReducs (e.g RunUMAP), the key gets truncated at the first underscore. Additionally, if it ends with a number (e.g. key.name = "umap_test2"), this causes bugs as the number at the end can get appended to the dimension number (e.g. dimension 1 becomes dimension 21).
If fewer features (or reduced dimensions) than the number of UMAP components to compute are passed, stop and display more informative error message. For example, hopefully prevents confusion in cases like RunUMAP(object, dims = 10)
…in SCTransform docs
Better input checking for RunUMAP
bug fixes for keys with underscores
sct transfer cca
Link to sctransform methods that populate slots of SCTransform output
Prep for CRAN release of 3.1.3
satijalab
approved these changes
Feb 11, 2020
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Patch to get Seurat back on CRAN, see our NEWS file for more details.
Addresses #2589