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Changelog

Source: NEWS.md

clustree 0.5.1 (2023-11-05)

CRAN release: 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 (2022-06-24)

CRAN release: 2022-06-25

Minor changes

Development versions

clustree 0.4.4.9001 (2022-06-24)

clustree 0.4.4 (2021-11-06)

CRAN release: 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 (2020-06-12)

CRAN release: 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)

clustree 0.4.2 (2020-01-29)

CRAN release: 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

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)

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 (2019-08-19)

CRAN release: 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)

CRAN release: 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)

CRAN release: 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)

clustree 0.3.0.9001 (2019-04-27)

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

clustree 0.2.2 (2018-07-10)

CRAN release: 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)

CRAN release: 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)

CRAN release: 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 (2018-04-11)

CRAN release: 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)

clustree 0.1.2.9005 (2018-06-23)

clustree 0.1.1 (2018-03-23)

CRAN release: 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 (2018-03-01)

  • First release
  • Remove theme_clustree() function

clustree 0.0.0 (2018-01-22)

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