R/qtl2 version 0.28

[Karl Broman]

A new version of R/qtl2 (version 0.28) has been released on CRAN. Windows and Mac binaries will be available within a few days. The major changes are below; a complete list of changes is at https://github.com/rqtl/qtl2/blob/main/NEWS.md

• The default colors for the Collaborative Cross (CC) have been changed to a color-blind friendly palette. The original CC colors remain as CCorigcolors; the previous default is now CCaltcolors.
• plot_coefCC() was revised to include col=CCcolors as an argument. The default is the new color-blind friendly CC colors, but one can now more easily use col=CCaltcolors or col=CCorigcolors to get a different choice.
• Added plot_sdp() to plot the strain distribution patterns of SNPs using tracks of tick-marks for each founder strain.
• Added arguments sdp_panel and strain_labels to plot_snpasso() so that you can include the plot_sdp() panel with the SNP association results and/or the genes.

Karl Broman

[Karl Broman]

The updated R/qtl2 package seems to need the latest version of the Rcpp package (1.0.7).

See https://github.com/rqtl/qtl2/issues/204

You can update both with the following:

    update.packages(oldPkgs=c("qtl2", "Rcpp"))

karl