Changes in version 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)

                 Changes in version 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)

                 Changes in version 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

                 Changes in version 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)

                 Changes in version 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

                 Changes in version 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)

                 Changes in version 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)

                 Changes in version 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)

                 Changes in version 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

                 Changes in version 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

                 Changes in version 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

                 Changes in version 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()

                 Changes in version 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

                        Changes in version 0.1.0                        

  - First release
  - Remove theme_clustree() function

                        Changes in version 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