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)

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 0.2.2.9000 (2018-08-01)

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

clustree 0.2.2.9001 (2018-08-06)

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

clustree 0.2.2.9002 (2019-02-02)

• Add show_axis argument

clustree 0.2.2.9003 (2019-02-12)

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

clustree 0.2.2.9004 (2019-02-17)

• Add ability to add additional node labels

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 0.2.1 (2018-07-09)

• Bump version for CRAN

clustree 0.2.1.9000 (2018-07-10)

• Replace SingleCellExperiment and Seurat example datasets with a list

clustree 0.2.1.9001 (2018-07-10)

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

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 (2018-04-11)

• 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 (2018-03-23)

• 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