k_modes() and CSPA()
consensus functions (#157)mixedClust instead of blockcluster for
co-clustering since the latter keeps getting archivedtestthat::skip_if_not_installed() to run tests
conditionally when using packages in Suggests@examplesIf and
rlang::is_installed() to run examples conditionally when
using packages in Suggestsblockcluster package as it is under active
maintenance againSuppress new names messages from transformed NMF data
Flattened matrices include 4th dimension of clustering array
Add package logo using hexSticker
Package blockcluster has been archived, remove from
Suggests
Remove deprecated context() in tests
Add RColorBrewer to Suggests because it is cross
referenced in ?graphs
Add trailing slash for URLs in DESCRIPTION
Remove tibble from Imports, no longer used
Suppress warnings when clValid::connectivity() is
called regarding comparison with more than one class. Since R-4.0.0, a
matrix object also inherits from class
array
In algii_heatmap(), the object ii
already has row names passed from columns which are named vectors (issue
also identified in #148, thanks @romainfrancois)
The following steps were taken to minimize dependencies and ensure
that diceR can still run on R 3.5:
Removed cli and RColorBrewer from
Imports
Moved apcluster, blockcluster,
cluster, dbscan, e1071,
kernlab, and kohonen to Suggests,
use their specific clustering algorithms conditionally.
mclust needs to be in Imports because
mclust::mclustBIC() needs to be imported
Moved sigclust to Suggests, use within
sigclust() conditionally
Moved progress to Suggests, use within
consensus_cluster() conditionally
Moved poLCA to Suggests, use within
dice() conditionally
Moved Rtsne to Suggests, use within
prepare_data() conditionally
Removed old dependency grDevices from
Imports
Set minimum version to R (>= 3.5) for klaR
dependency questionr
In ev_confmat(), use
yardstick::conf_mat() instead of
caret::confusionMatrix(). caret has many
dependencies, so best to avoid using it
In graph_heatmap(), use NMF::aheatmap()
instead of gplots::heatmap.2(). gplots depends
on caTools, which now relies on R (>= 3.6)
In consensus_cluster(), use
stringr::str_to_title() instead of
Hmisc::capitalize(). Hmisc depends on
latticeExtra, which now relies on R (>= 3.6)
In graph_delta_area(), use base solution instead of
flux::auc(). flux also depends on
caTools
In prepare_data(), use own implementation of
quantable::robustscale() with all of the former function’s
defaults. quantable also depends on
caTools
Specify Bioconductor installation on Travis and AppVeyor since
NMF now Imports Biobase
Remove suppressWarnings(RNGversion("3.5.0")) after
updating R version
Run LCA() unit test on imputed clustering
object
Remove internal validity measures with any Inf
entries for consensus_reweigh()
Use a cleaner, more robust method of removing
Rplots.pdf after running
test-graphs.R
Ensure column binding with purrr::map_dfc() in
consensus_rank()
Replaced dplyr::bind_cols() with
purrr::flatten_dfc() to suppress warning “Outer names are
only allowed for unnamed scalar” in get_cdf()
update roxygen and docs
Remove deprecated dplyr functions and use
.data pronoun
k-means clustering should not support distance matrices as input (@jerryji1993, #139)
Add LCA as a consensus function (@philstraforelli, #137)
Fix length > 1 in coercion to logical error in
consensus_evaluate() due to comparisons using
|| operator
Add suppressWarnings(RNGversion("3.5.0")) before
call to set.seed() in examples, tests, and vignette to use
old RNG sampling
Use .covrignore to exclude zzz.R from
being considered in code coverage
Use dplyr version >= 0.7.5 to ensure
bind_rows() works
Fixed bug where scaled matrix using the “robust” method in
prepare_data() was nested in the data element
(@AlineTalhouk,
#134)
Add parameter hc.method in dice and
consensus_cluster to pass to method parameter
in stats::hclust (@JakeNel28, #130)
Remove dependencies on largeVis: package will be
archived
Revert back to using NMF since NNLM has
been archived and NMF is back in active
maintenance.
Choose fuzzifier m in cmeans using Equation 5 from
https://academic.oup.com/bioinformatics/article/26/22/2841/227572
(thanks @Asduveneck)
Replace all code that depended on NMF with
NNLM and pheatmap: CRAN notified that
NMF will be archived because of inactive
maintenance
Update .yml files default templates
Fix bug in consensus_cluster() when custom
algorithms were excluded from output (thanks @phiala)
Use markdown language for documentation
Various performance improvements and code simplifications
Suppress success/fail message printout and fix input data to be matrix for block clustering
Fix bug in algii_heatmap() when
k.method = "all" in dice()
Fix bug in calculating internal indices when data has categorical variables (thanks Kurt Salmela)
Updated object output names in
consensus_evaluate()
Fix unit test in test-dice.R for R-devel
Add internal function: ranked algorithms vs internal validity indices heatmap graph
Fix bugs in graph_cdf(),
graph_tracking() when only one k selected
Progress messages in dice()
Fix bug in consensus_evaluate() when algorithm has
NA for all PAC values
New dimension reduction methods: t-SNE, largeVis (@dustin21)
Better annotated progress bar using progress
package
Speed up the operation that transforms a matrix to become “NMF-ready”
Simplify saving mechanism in consensus_cluster()
such that only file.name needs to be specified, and the
save parameter has been removed
New algorithms: SOM, Fuzzy C-Means, DBSCAN (@dustin21, #118)
Added significance testing section to vignette
Fixed direction of optimization: compactness and connectivity should be minimized