The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
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
(2022-06-24)
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
(2021-11-06)
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)
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
(2019-08-19)
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)
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)
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
(2018-04-11)
- 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)
clustree 0.0.0.9001
(2018-01-23)
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)
clustree 0.0.0.9008
(2018-01-27)
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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.