Changelog

signals 0.17.0

  • Breaking: fix the Viterbi backtrace in viterbi() (C++) and viterbiR(). It seeded the final bin with the predecessor of the best final state and then backtracked from the per-column argmax instead of following the stored backpointers, so it did not return the most likely path and emitted spurious single-bin state changes. Single-bin sequences also decoded to state 0 (C++) or errored (R). This changes haplotype- and allele-specific copy number calls: on a 725-cell DLP+ sample (chr6, analysis from #79) 194 cells changed path, 0.30% of bins changed, and mean A/B segments per cell fell from 1.71 to 0.26. Use signals 0.16.0 to reproduce earlier results.
  • Fix alleleHMM producing all -Inf emissions for homozygous-deletion bins (total CN 0), which forced the rest of the chromosome to minor CN 0.
  • Fix createCNmatrix(centromere = TRUE): masking is now gated on fillnaplot, so it no longer errors with fillna = TRUE and actually runs with fillnaplot = TRUE.

signals 0.16.0

  • Add sv_arcs_above to plotCNprofile: draw SV arcs in a band above the copy number panel rather than on top of it, split by copy number effect with apex scaled by genomic span
  • Fix SVs with both breakends in the same bin being silently dropped, which lost every foldback at 10kb resolution
  • Fix panels with no SVs not reserving the SV band, so stacked panels stay aligned
  • Add show_chrbreaks and ybreaks options to plotCNprofile
  • Fix multi-region tick marks so each region gets a tick at its start, and dividers bracket both region edges
  • Add multi-region plotting support to plotCNprofile
  • Add y-axis transform option for the mean/IQR heatmap track
  • Fix ordered_cell_ids initialisation in plotHeatmap
  • Add SVs example data (destruct breakpoints for SA921, the sample CNbins comes from) and a structural variant visualization vignette
  • Document all bundled datasets, which had no help pages

signals 0.15.0

  • Add configurable annotation colour overrides for discrete and continuous annotation columns
  • Add configurable continuous/discrete threshold handling and robust cell matching for annotation metadata
  • Add a mean + IQR top summary track, with support for sourcing that track from a different column than the heatmap
  • Refine SV orientation colours and document the new plotHeatmap options

signals 0.14.1

  • Fix rephasebins stability to ensure stable results

signals 0.14.0

  • Add gene annotation feature to plotHeatmap with customizable positions and styling
  • Add chromosome ideogram (cytoband) visualization at the bottom of heatmaps
  • Add plotideogram and plotallbins parameters to visualize centromeric regions
  • Improve frequency annotation handling for BAF and state plots

signals 0.13.1

  • Fix plotHeatmap annotation handling for data.table/tibble inputs

signals 0.13.0

  • Add SV visualization with lines and arcs style showing orientation
  • Add automatic position and strand correction for SV data with reversed coordinates
  • Add SV legend support for orientation color coding
  • Fix SV read count axis scaling issues

signals 0.12.0

  • option to input cells to use for phasing for each chromosome
  • plotHeatmap with arbitrary annotation dataframe
  • remove chrY

signals 0.11.4

  • fix typo assigning A->B

signals 0.11.3

  • catch negative state_AS issue for singleton bins

signals 0.11.2

  • fix negative state_AS issue. This was caused during the fill missing step which assigns states with NA BAF values based on neighbouring bins. When there was a state transition between bins sometimes A+B>state.

signals 0.11.1

  • for umap_clustering, default is now to not use PCA

signals 0.11.0

  • updates to plotting
  • male/female option
  • filter some cell for second pass phasing but do not remove
  • do not remove cells by default if they have low coverage
  • keep cells with large hom-dels

signals 0.10.0

  • add chr string check
  • remove acrocentric chromosomes in arm consensus
  • minor changes to heatmap and plotting

signals 0.9.1

  • Update docker to install suggests packages

signals 0.9.0

  • Fix phasing issue that happens when the cluster identified to phase relative to has a diploid region

signals 0.8.0

  • Add option to mask bins during inference

signals 0.7.6

  • Fix bug in plot_clusters_used_for_phasing

signals 0.7.5

  • Fixed r cmd check

signals 0.7.4

signals 0.7.3

signals 0.7.2

  • release for zenodo

signals 0.7.1

signals 0.7.0

  • change name to signals
  • multiple updates to plotting
  • rewrite of scRNAseq

signals 0.6.2

  • fix missing argument

signals 0.6.1

  • changed colours
  • fill in missing bins
  • improved documentation about inputs

signals 0.6.0

  • add option to remove noisy cells from phasing

signals 0.5.5

  • update plotting and clustering

signals 0.5.4

  • update docker

signals 0.5.3

  • some small updates to plotting and default params

signals 0.5.2

  • update to vignette and plotting

signals 0.5.1

  • updated default parameters

signals 0.5.0

  • update ascn inference

signals 0.4.3

  • filtering utility function

signals 0.4.2

  • fix bug with filtering

signals 0.4.1

  • Fix bug in HMM when total copy number = 0
  • Add function to filter hscn object

signals 0.4.0

  • Add option to filter haplotypes
  • Added Dockerfile and github actions to push to Dockerhub
  • Added QC metadata table to output

signals 0.3.0

  • Version associated with preprint
  • some fixes to plotting

signals 0.2.1

  • updates to heatmap plotting

signals 0.2.0

signals 0.1.0

  • Added a NEWS.md file to track changes to the package.