seriation_1.3-0

Changes

• Plotting
  • Most plotting functions have now a common interface. This changed many parameters.
  • hmap now uses heatmap from package stats.
  • dissplot shows now averages in the top triangles.
  • improved layout (less white space) for grid-based plots.
• Registry
  • list_seriation_methods and list_criterion_methods without kind return now a list.
  • show_seriation_methods and show_criterion_methods are deprecated
• Other Changes
  • criterion returns now NA with a warning for ME for non-positive matrices (used to stop with an error).
  • dependency dendextend is now only suggested (used for testing).
  • get_order now returns also labels.
  • hclust-based seriations now defaults for linkage to complete instead of average.

New Features

• Plotting
  • Major refactoring of plotting functions to provide a more consistent interface.
  • added ggplot2-based plots, ggimage, gghmap, ggVAT, ggiVAT, ggbertinplot, ggdissplot.
  • colors are now more consistent and all have bias and power.
• Seriation methods
  • seriate for matrix has now method "Heatmap".
  • seriate now accepts data.frames and used method "heatmap" as the default.
  • added seriation method "Reverse" for reverse identity order.
• Permutation
  • permute for matrix-like objects gained parameter margin.
  • permute for data.frame works now identical to permute for matrix.