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CHANGELOG.md

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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