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Showing content from http://cran.rstudio.com/web/packages/rJava/../matchingMarkets/../ggplot2/../clustree/news/news.html below:

NEWS

• Minor updates for compatibility with Seurat >= 5.0.0 and ggplot2 >= 3.4.0

• Avoid warnings due to deprecated functionality in ggplot2 and tidyselect. Includes increasing the ggplot2 requirement to >= 3.4.0. (Fixes #35)

• Minor updates for compatibility with upcoming Seurat v5 release (Fixes #93)

• Add node_text_angle argument to clustree() (Fixes #79, PR #80)

• Add node_text_angle argument to clustree() (Fixes #79, PR #80)

• Minor changes to tests which were failing due to changes in the Bioconductor 3.14 release
• Minor updates to URLs in documentation

• Fix axis label order in clustree() (Fixes #44)
• Add checks to handle features including “-” characters for Seurat and SingleCellExperiment interfaces to clustree() and clustree_overlay() (Fixes #43)
• Change how metadata columns are extracted for compatibility with tibble objects (Fixes #52)

• Replace the iris_clusts dataset with the nba_clusts dataset
• Increase R dependency to > 3.5

• Change how metadata columns are extracted for compatibility with tibble objects (Fixes #52)

• Replace the iris_clusts dataset with the nba_clusts dataset

• Add checks to handle features including “-” characters for Seurat and SingleCellExperiment interfaces to clustree() and clustree_overlay() (Fixes #43)

• Fix axis label order in clustree() (Fixes #44)

• Fix bug where the sc_example dataset required loading additional libraries as notified by CRAN (Fixes #40)
  • sc_example contained a DataFrame rather than a data.frame for the SC3 data, this has now been fixed
• Add fixed alpha scale range to clustree_overlay() (Fixes #41)
  • Alpha will now represent in_prop values between 0 and 1
• Change how point colour resolution name is determined for side plots in clustree_overlay() (Fixes #38)
• Fix missing alpha scale in clustree() (Fixes #32)
• Change prefix matching to simpler exact method without regular expressions
  • This should allow matching the start of column names without the wildcard problem in Issue #19
• Fixes for minor bugs discovered with new unit tests

• Add additional unit tests, including some missing from clustree_overlay()
  • Tests for matching prefix values
  • Test for point colour in clustree_overlay() with rounded resolutions

• Add additional unit tests, including some missing from clustree_overlay()
• Minor fixes for bugs discovered with new tests

• Add additional unit tests

• Add fixed alpha scale range to clustree_overlay() (Fixes #41)

• Add tests for matching prefix values
• Change prefix matching to simpler exact method without regular expressions
• Add test for point colour in clustree_overlay() with rounded resolutions
• Change how point colour resolution name is determined (Fixes #38)

• Fix missing alpha scale (Fixes #32)

• Fix bug where the sc_example dataset required loading additional libraries (Fixes #40)
  • sc_example contained a DataFrame rather than a data.frame for the SC3 data

• Remove requirement for clustering matrix to be numeric (Fixes #33)
• Fix bug where sc3_stability became character with character cluster names
• Keep order when all cluster names are numeric
• Improve how reducedDims are accessed on SingleCellExperiment objects
• Fix minor typos in documentation

• Improve how reducedDims are accessed on SingleCellExperiment objects
• Fix minor typos in documentation

• Fix bug where sc3_stability became character with character cluster names
• Keep order when all cluster names are numeric

• Remove requirement for clustering matrix to be numeric (Fixes #33)

• Add support for Seurat v3 objects (thanks to @mojaveazure)
• Add SC3 stability index section to vignette (Fixes #28)

• Make the cluster node attribute a factor to improve use as node colour (Fixes #20)
• Add show_axis argument that displays the y-axis with resolution values and gridlines (Fixes #24)
• Add ability to add additional node labels with custom information (Fixes #23)
• Update CITATION to give information about the GigaScience paper
• Update README
• Update vignette
  • Add custom labels section
  • Add references
  • Add table of contents and number sections

• Add checks for metadata column and node aesthetic names (Fixes #15)
• Use fixed patterns when identifying clustering columns in data.frames (Fixes #19)

• Add support for Seurat v3 objects (thanks to @mojaveazure)

• Add SC3 stability index section to vignette (Fixes #28)

• Replace SingleCellExperiment and Seurat example datasets with a list
• Add additional checks for suggested packages
• Remove links to suggested packages in documentation

• Update CITATION
• Update README
• Add spelling checks
• Update vignette
  • Add custom labels section
  • Add references
  • Add table of contents and number sections

• Add ability to add additional node labels

• Add checks for metadata column and node aesthetic names
• Adjust show_axis to use gridlines

• Add show_axis argument

• Make the cluster node attribute a factor to improve use as node colour

• Use fixed patterns when identifying clustering columns in data.frames

• Bump version for CRAN

• Add additional checks for suggested packages
• Remove links to suggested packages in documentation

• Replace SingleCellExperiment and Seurat example datasets with a list

• Calculate the SC3 stability index for cluster nodes
• Improvements to the clustree() function:
  • Add option to use core network to calculate layout
  • Add option to highlight core network
  • Add option to return plot, graph or layout
• New clustree_overlay() function
  • Allows overlaying of clustering trees on other data dimensions
• Store trees as tbl_graph instead of igraph objects
• Switch to GPL-3 license
• Updates to vignette, documentation and tests

• Adjust tests to work with new checkmate version (v1.8.6)
• Update R requirement to >= 3.4 (for compatibility with SingleCellExperiment)
• Add CITATION file and update author entries in DESCRIPTION

• Add functions to calculate the SC3 stability index
• Switch to GPL-3 license

• Add option to use core network to calculate layout
• Add option to highlight core network
• Add option to return plot, graph or layout

• Store tree as tbl_graph instead of igraph object
• Update vignette

• Add checks for suggested packages

• Add clustree_overlay() function

• Add plot_sides argument to clustree_overlay()

• Add edge_arrow_ends argument

• Adjust tests to match checkmate messages

• Update R requirement to >= 3.4

• Add CITATION file
• Update author entries in DESCRIPTION

• First release
• Remove theme_clustree() function

• Start development

• Implement basic plotting

• Add node aesthetic options

• Add more control over aesthetics

• Add SingleCellExperiment example data
• Add SingleCellExperiment method

• Add Seurat example data
• Add Seurat method

• Add documentation
• Add parameter checks

• Add tests and run checks

• Add vignettes

• Add data option to exprs for Seurat objects

• Check that at least two resolutions have been provided
• Add node text colour option
• Improve example scRNA-seq datasets

• Fix missing node when all aesthetics static

• Switch from using function for aggregation to function names
• Improve naming of aesthetics
• Set alpha scale limits
• Add Sugiyama layout
• Update vignette
• Tidy code

• Fix resolution colour ordering

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