NEWS.md

In mixOmicsTeam/mixOmics: Omics Data Integration Project

version 6.18.0

new features / enhancements / changes

• new function plotMarkers to visualise the selected features in block analyses (see #134)
• auroc title now fixed (#135)
• cimDiablo takes trim argument to customise outlier filtering (#136)
• plotIndiv.pca default shape set to 16
• circosPlot & network now support blocks with similar feature names
• circosPlot now has methods for block.spls objects
• circosPlot now takes new formal and advanced args for customisation. See ?circosPlot.

bug fixes

• plotVar legend colour mismatch bug fixed
• plotDiablo error undefined variable (Y) fixed
• nipals initialisation bug with high-variance high-NA rate column fixed
• cim bug with high NA rate data fixed using imputation by the column mean

version 6.16.0

new features / enhancements / changes

• biplot default colours now match plotIndiv
• biplot now takes cex argument
• nipals now takes center and scale arguments
• nipals now only outputs p, t and eig
• new function impute.nipals to impute missing values using NIPALS algorithm
• nipals function checks for orthogonality of components when NA present
• plot.tune legends improved
• plot.tune now uses colour-blind friendly colours
• new tune.spls function to perform variable selection on both X and Y
• tune.spls now chooses optimal keepX even if nrepeat < 3
• tune.spls now takes validation arg
• tune.spca is now much faster
• circosPlot links can now have adjustable width (#118)
• plotDiablo now takes col.per.group (#119)
• terminology change: consensus renamed to average in Diablo context

bug fixes

• plotVar bug fixed

version 6.14.0

new features / enhancements / changes

• circosPlot: The radial location of feature names can now be cutomised using var.adj
• added plot and print methods for nipals ouput (#87)
• all Discriminat Analyses now run solely on mode=regression (#79)
• cim argument change: threshold replaced by cutoff
• nipals and pca with missing values allow skipping reconstitution of the input matrix
• tune.block.splsda now allows random number seed also for parallel processing (#72)
• New biplot methods for the pca family (#90)

bug fixes

• plotIndiv: Legend bug which misspecified the groups resolved
• plotIndiv: Legends now ordered as inputted, and not alphabetically
• plot method issue for spca resolved
• plotLoadings.spca bug with var.names now fixed (#81)
• ipca deprecation warning fixed

version 6.12.0

new features / enhancements

• plotLoadings's infamous figure margins too large error now handled and informative condition thrown
• circosPlot's lines argument default to FALSE now
• circosPlot's inconsistentcy of blocks with identical X names fixed
• consensus and weighted consensus plots now supported for plotIndiv with relevant block analyses
• plotLoadings's feature name trimming can be customised
• block.splsda bug which could drop some Y factors with near.zero.variance=TRUE fixed
• perf.block.splsda now supports calculation of combined and per-block AUC
• model improvement significance can be custmoised in all perf and tune functions
• perf.block.splsda is now much faster and supports FORK clusters
• tune.(s)pls(da), perf.(s)plsda now support FORK clusters

bug fixes

• circosPlot's faded lines bug when many NAs present fixed
• tune.block.splsda() bug when using fixed test.keepX over two or more blocks fixed
• circosPlot and plotLoadings bug caused by features with NAs fixed
• plotIndiv(..., ind.names = FALSE) warning/bug fixed
• tune.block.splsda bug on Windows parallelisation fixed
• perf and tune functions' issue when choosing the optimum component resolved
• added option to suppress auroc from printing all the AUCs

version 6.10.0

new features / enhancements

• parallel processing on tune.block.splsda improved
• tune.block.splsda now supports more distances
• You can now customise auroc plots. Refer to documentation for more info

bug fixes

• single factor multilevel error in pls fixed
• fixed over-estimated correlation of cim for mixo_(s)pls objects with single component
• margin error in cim now handled properly
• fixed plotLoadings error for very long variable names
• predict function bug for single sample prediction fixed
• plotLoadings bug for long variable names fixed
• Fixed tune.spls and pef.plsda bugs when using cpus argument for parallel processing
• perf.plot bug in extracting names fixed
• Few fixes for tune.splsda with AUC

minor improvements

• missing values in plotIndiv's group argument no more throws error
• mixOmics::predict function documentation now more accessible
• names of linnerud datasets fixed
• plot.perf now respects ylim arguments for custom y range
• package startup message with direct liks to useful resources
• mixOmics function documentation disambiguated with instruction on how to get package help
• Updated onLoad message with discussion forum info, bug reports, and more
• Dropped legacy comp.tol argument from pca
• plot.perf now respects ylim arguments for custom y range
• Added Code of Conduct

version 6.8.0

• NOW HOSTED ON BIOCONDUCTOR

version < 6.8.0

• Refer to ./inst/legacy/NEWS-old on GitHub repo

mixOmicsTeam/mixOmics documentation built on Nov. 4, 2024, 8:56 a.m.