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CHANGELOG.md

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[1.3.0] - 2020-19-3

Changed

  • Moved some code to the new package sccore
  • Fixed inconsistent use of parameters for different spaces in buildGraph
  • Various small fixes
  • Fixed the number of components calculated for the simple PCA rotation
  • Conos is R6 class now (instead of refClass)

Added

  • Functionality for PAGA graph collapsing
  • Parameters k.same.factor and balancing.factor.per.sample to buildGraph. It can be used to improve alignment between different conditions: with same.factor.downweight it gives the system similar to k.self and k.self.weight
  • plotDEheatmap() function for viewing marker genes
  • Function convertToPagoda2 to create Pagoda 2 from Conos. Helpful for PagodaWebApp.

[1.2.1] - 2019-12-3

Changed

  • Fixed getDifferentialGenes
  • Fixed testing clustering stability

[1.2.0] - 2019-11-27

Changed

  • Added mean M value column to the diff. expression output
  • Optimized plotting with coloring by genes
  • getDifferentialGenes uses first clustering by default
  • Fixed bug with collapseCellsByType. Note: probably will affect DE results.
  • Added re-normalization of edge weights to fix problem with negative edge weights during label propagation
  • Now in plotting 'groups' aren't ignoted if 'gene' is provided: it's used to subset cells for plotting.
  • UMAP now set n_sgd_threads from uwot to n.cores by default. It gives much better parallelization, but kills reproducibility. Use n.sgd.cores=1 to get reproducible embeddings.
  • Account for target.dims in UMAP embedding
  • Fixed estimation of cor.based with alingnment.strength == 0. It removes edges with negative correlation and reduce down-weight of inter-sample edges, which can change results of the alignment.
  • Changed default value of fixed.initial.labels in propagateLabels from FALSE to TRUE. Presumably, FALSE should never be used.
  • New output format for label propagation (list of "labels", "uncertainty" and "label.distribution")
  • Numerous small bug fixes and small validations for correct arguments
  • ScanPy integration tutorials to refelect the changes in saveConosForScanPy

Added

  • Metrics to masure specifisity of cell type markers to DE info in getDifferentialGenes (parameters append.specifisity.metrics and append.auc)
  • Implementation of label propagateion based on matrix equations (occured to be too slow)
  • Function findSubcommunities to increase resolution for specific clusters
  • Parameter subgroups to embeddingPlot. It allows to plot only cells, belonging to the specified subgroups
  • Parameter keep.limits to embeddingPlot
  • Added metrics to masure specifisity of cell type markers to DE info in getDifferentialGenes (parameters append.specifisity.metrics and append.auc)
  • velocityInfoConos function for RNA velocity analysis on samples integrated with conos (together with supplementary functions prepareVelocity and pcaFromConos)
  • "Running RNA velocity on a conos object" section in README.md (explains usage of the velocityInfoConos function)
  • Function getJointCountMatrix to conos obect
  • New possibilities to customize the output of saveConosForScanPy
  • Function parseCellGroups to parse properly cell groupings depending on user settings
  • Function estimteWeightEntropyPerCell to visualize alignment quality per cell

[1.1.2] - 2019-07-16

Changed

  • Changed a description line in the getClusterPrivacy() doc to fix installation under some R3.6 versions (issue 32)

[1.1.1] - 2019-07-15

Changed

  • Fixed docker build: use of BiocManager, reference to master instead of dev
  • Updated src/Makevars to remove the CXX directive, which trips up older versions of R (3.2.x)

[1.1.0] - 2019-07-02

Added

  • Support for CCA space

Changed

  • buildGraph now use PCA space as the default
  • fixed common variance rescaling to use geometric mean of the target

[1.0.3] - 2019-07-02

Added

  • Support for Seurat v3 objects

[1.0.2] - 2019-06-26

Added

  • Functions to export Conos object to ScanPy

[1.0.1] - 2019-05-1

Fixed

  • Default value for cluster.sep.chr in DE functions is changed from '+' to '<!!>', as it shouldn't be normally present in cluster names
  • Removed Boost dependency
  • Fixed version of Seurat and fpc packages in Docker

[1.0.0] - 2019-04-17

Fixed

  • Fixed ggplot2 namespace for function calls in plotClusterStability
  • Renamed stable.tree.clusters, get.cluster.graph and scan.k.modularity
  • Removed exports of largeVis internals, get.cluster.graph and get_nearest_neighbors
  • embedding is stored with samples by rows now (i.e. not transposed anymore)
  • Using scale.data instead of data in Seurat if provided

Deprecated

  • multitrap.community and multimulti.community functions

[0.1.0] - 2019-04-17

Added

  • Pre-release version