NEWS

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clustree 0.5.1 (2023-11-05)

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

Development versions

clustree 0.5.0.9001 (2023-10-24)

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

clustree 0.5.0.9000 (2023-10-24)

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

clustree 0.5.0 (2022-06-25)

Minor changes

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

Development versions

clustree 0.4.4.9001 (2022-06-24)

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

clustree 0.4.4 (2021-11-08)

Bug fixes

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

clustree 0.4.3 (2020-06-14)

Bug fixes

• 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)

Other changes

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

Development versions

clustree 0.4.2.9003 (2020-06-12)

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

clustree 0.4.2.9002 (2020-06-12)

• Replace the iris_clusts dataset with the nba_clusts dataset

clustree 0.4.2.9001 (2020-03-20)

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

clustree 0.4.2.9000 (2020-03-19)

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

clustree 0.4.2 (2020-01-29)

Bug fixes

• 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

Other changes

• 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

Development versions

clustree 0.4.1.9005 (2020-01-29)

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

clustree 0.4.1.9004 (2020-01-28)

• Add additional unit tests

clustree 0.4.1.9003 (2020-01-28)

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

clustree 0.4.1.9002 (2020-01-28)

• 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)

clustree 0.4.1.9001 (2020-01-27)

• Fix missing alpha scale (Fixes #32)

clustree 0.4.1.9000 (2020-01-27)

• 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

clustree 0.4.1 (2019-08-21)

Bug fixes

• 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

Development versions

clustree 0.4.0.9002 (2019-08-19)

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

clustree 0.4.0.9001 (2019-06-05)

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

clustree 0.4.0.9000 (2019-06-03)

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

clustree 0.4.0 (2019-04-18)

Minor changes

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

clustree 0.3.0 (2019-02-24)

Minor changes

• 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

Bug fixes

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

Development versions

clustree 0.3.0.9000 (2019-04-27)

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

clustree 0.3.0.9001 (2019-04-27)

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

clustree 0.2.2 (2018-07-10)

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

clustree 0.2.2.9005 (2019-02-24)

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

clustree 0.2.2.9004 (2019-02-17)

• Add ability to add additional node labels

clustree 0.2.2.9003 (2019-02-12)

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

clustree 0.2.2.9002 (2019-02-02)

• Add show_axis argument

clustree 0.2.2.9001 (2018-08-06)

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

clustree 0.2.2.9000 (2018-08-01)

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

clustree 0.2.1 (2018-07-09)

• Bump version for CRAN

clustree 0.2.1.9001 (2018-07-10)

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

clustree 0.2.1.9000 (2018-07-10)

• Replace SingleCellExperiment and Seurat example datasets with a list

clustree 0.2.0 (2018-06-24)

• 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

clustree 0.1.2 (2018-04-20)

• 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

clustree 0.1.2.9000 (2018-05-08)

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

clustree 0.1.2.9001 (2018-05-09)

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

clustree 0.1.2.9002 (2018-05-22)

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

clustree 0.1.2.9003 (2018-06-20)

• Add checks for suggested packages

clustree 0.1.2.9004 (2018-06-22)

• Add clustree_overlay() function

clustree 0.1.2.9005 (2018-06-23)

• Add plot_sides argument to clustree_overlay()

clustree 0.1.1 (2018-03-27)

• Add edge_arrow_ends argument

clustree 0.1.1.9000 (2018-04-11)

• Adjust tests to match checkmate messages

clustree 0.1.1.9001 (2018-04-11)

• Update R requirement to >= 3.4

clustree 0.1.1.9002 (2018-04-11)

• Add CITATION file
• Update author entries in DESCRIPTION

clustree 0.1.0

• First release
• Remove theme_clustree() function

clustree 0.0.0

clustree 0.0.0.9000 (2018-01-22)

• Start development

clustree 0.0.0.9001 (2018-01-23)

• Implement basic plotting

clustree 0.0.0.9002 (2018-01-24)

• Add node aesthetic options

clustree 0.0.0.9003 (2018-01-25)

• Add more control over aesthetics

clustree 0.0.0.9004 (2018-01-26)

• Add SingleCellExperiment example data
• Add SingleCellExperiment method

clustree 0.0.0.9005 (2018-01-27)

• Add Seurat example data
• Add Seurat method

clustree 0.0.0.9006 (2018-01-27)

• Add documentation
• Add parameter checks

clustree 0.0.0.9007 (2018-01-27)

• Add tests and run checks

clustree 0.0.0.9008 (2018-01-27)

• Add vignettes

clustree 0.0.0.9009 (2018-02-02)

• Add data option to exprs for Seurat objects

clustree 0.0.0.9010 (2018-02-05)

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

clustree 0.0.0.9011 (2018-02-09)

• Fix missing node when all aesthetics static

clustree 0.0.0.9012 (2018-02-15)

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

clustree 0.0.0.9013 (2018-02-28)

• Fix resolution colour ordering