CHANGELOG.md

In kharchenkolab/conos: Clustering on Network of Samples

Upcoming

[1.5.2] - 2024-26-February

• Removed -L/usr/lib/ in Makevars

[1.5.1] - 2024-22-January

• Remove C++11 flag
• Fixed various roxygen2 typos and variable names for docs consistency
• S3 method exports, buildWijMatrix.*

[1.5.0] - 2022-17-October

• Fixed compilation issue on certain OS configurations

[1.4.9] - 2022-29-September

• Fix multithreading with largeVis, GitHub issue #129

[1.4.8] - 2022-25-September

• Add back velocityInfoConos()
• Remove 'Matrix.utils' as dependency

[1.4.7] - 2022-04-September

• Fixes for Matrix, updated versions 1.4.2, 1.5.0
• Use inherits() for conditionals with class()

[1.4.6] - 2022-30-March

• Fixed bug with snn argument in buildGraph() due to the parameter snn.k.self
• Fixed bug in getDifferentialGenes() based on warnings from sccore::plapply()

[1.4.5] - 2022-20-January

Changed

• Removed unused R packages from "Suggests" (now in sccore), i.e. 'ggrastr', 'pROC', 'pbapply'
• Modified adjustedRand.c from clues to C++ function, revised R code for internal function adjustedRand() in conclass.R

[1.4.4] - 2021-08-November

Changed

• Added fail.on.error=TRUE in some plapplys
• Re-added getGeneExpression() methods for Seurat (lost in merge 552408f)
• Switched to CircleCI

[1.4.3] - 2021-02-August

Changed

• Fix the function parseCellGroups(), check if clustering exists

[1.4.2] - 2021-28-June

Changed

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

[1.4.1] - 2021-14-May

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

[1.4.0] - 2021-23-Feb

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
• auxilliary package conosPanel used

Removed

[1.3.1] - 2020-24-09

Changed

• allow multiple embeddings in conclass (July 2020)
• Improved plotDEheatmap function
• Fixed bug with balancing.factor.per.sample in buildGraph
• Fixed some installation problems
• Improve R6 documentation
• Changed std::cout to Rcpp::Rcout (July 2020)
• Revised README, vignettes (July 2020)

Added

• multiple embeddings in Conos object (July 2020)
• Write to HDF5 for saveConosForScanPy() (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)
• LICENSE (July 2020)

Removed

• Removed getCorrectionVector() and getPerCellTypeDECorrected (2 July 2020)
• Removed all neighborhood averaging via neighborhood.average (4 July 2020)
• Removed raster.height and raster.width from con$plotEmbedding(), given these parameters are defunct with rewrite of ggrastr (v0.2.0)[https://github.com/VPetukhov/ggrastr/releases/tag/v0.2.0]

[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

kharchenkolab/conos documentation built on Feb. 28, 2024, 6:03 a.m.