Version 1.4.2

Version 1.4.2 published on CRAN, 29 June 2021

Changed

• Add scaling to scaledMatricesSeurat(), scaledMatricesSeuratV3()
• Change sccore::plapply() in updatePairs()

Version 1.4.1

Version 1.4.1 published on CRAN, 15 May 2021

Added

• support Seurat objects in getOdGenesUniformly and con$correctGenes

Removed

• functions collapseCellsByType and colSumByFactor are moved to sccore
• removed strong dependency on drat repositories; only used now for the vignettes in the README

Version 1.4.0

Changed

• extensive revisions for CRAN upload, including roxygen2 documentation
• replaced relevant C++ code and Rcpp functions with N2R and leidenAlg
• vignettes edits, detailing p2app4conos() for rendering Conos to pagoda2 application
• updated Dockerfile
• extensively revised vignettes and moved them, due to on CRAN build + check duration limits
• README revisions for clarity

Added

• added getGeneExpression() for Seurat v2 and v3 (January 2021)
• add parameter raster.dpi in con$plotEmbedding() to replace raster.height and raster.width, given these parameters are defunct with *rewrite of ggrastr (v0.2.0)[https://github.com/VPetukhov/ggrastr/releases/tag/v0.2.0]
• Rjnmf added as Rcpp function
• auxiliary package conosPanel used

The initial CRAN version for conos 1.4.0 was published on Feb 23 2021: https://cran.r-project.org/web/packages/conos/index.html

Version 1.3.1

[1.3.1] - 2020-24-09

Changed

• Improved plotDEheatmap function
• Fixed bug with balancing.factor.per.sample in buildGraph
• Fixed some installation problems
• Improve R6 documentation
• Installs on Mac OS

Added

• Changed std::cout to Rcpp::Rcout (July 2020)
• Revised README, vignettes (July 2020)
• added ht_opt$message = FALSE for ComplexHeatmap (July 2020)
• Added checks for getPerCellTypeDE() for errors, removing NAs (July 2020)
• Added ht_opt$message = FALSE for ComplexHeatmap (July 2020)
• Write to HDF5 for saveConosForScanPy() (July 2020)
• LICENSE (July 2020)

Removed

• Removed getCorrectionVector() and getPerCellTypeDECorrected (2 July 2020)
• Removed all neighborhood averaging via neighborhood.average (4 July 2020)

Version 1.3.0-1 (docker update)

Tag to update the docker version build

Version 1.3.0

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.

Version 1.2.1

Changed

• Fixed getDifferentialGenes
• Fixed testing clustering stability

Version 1.2.0

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