- Custom ordering of individual clusters within collated clusters. Earlier this
followed label ordering as per
cutree
output - Improved messages for model selection using cross-validation
- (User-facing) The agglomeration and distance method used for collation of clusters can be set as part of configuration settings
- (User-facing) Argument name
inner_chunk_size
changed tochunk_size
inarchR_set_config()
- Accounting and correcting for over-fitting improves clusters/architectures' quality
- Improved messages
- (User-facing) New function
collate_clusters()
- (User-facing) tolerance no longer an argument in archR_set_configuration
- Can choose to fix aspect ratio for visualization functions
plot_ggheatmap()
plot_ggseqlogo()
viz_bas_vec_heatmap_seqlogo()
viz_bas_vec_heatmap()
viz_bas_vec_seqlogo()
plot_arch_for_clusters()
plot_ggseqlogo_of_seqs()
- Ability to detect occurrence of just for sake clustering when fetching from HAC
- (User-facing) Getter functions to fetch archR result object elements.
seqs_str()
to fetch DNA sequences for a particular cluster, iteration etc.get_clBasVec()
to fetch basis vectors element at given iteration.get_clBasVec_k()
to fetch number of basis vectors/clusters.get_clBasVec_m()
to fetch basis vectors.get_seqClLab()
to fetch cluster Ids for each sequence.
- (User-facing) Arguments of all functions consistently use underscores.
- Fix staged installation error. This enables seamless installation on macOS.
- CI with GHA.
- (User-facing) archR result list has new elements:
timeInfo
if timeFlag is TRUE;clustSol
storing combined clusters from the last iteration of archR.
- (User-facing) Architectures/clusters sequence logos can be plotted with
auto
y-axis limits for information content (0-max instead of 0-2). - (User-facing) TFBSTools moved from dependency to suggests. This eases installation of archR by reducing possibility of failed installation.
- Accepts FASTA sequences as DNAStringSet object(s)