README.md

In andrewparkermorgan/mouser: Colour Schemes and Constants Related to Mouse Genetics

mouser

A simple package to define some colour schemes and constants useful for mouse genetics, with a focus on the Collaborative Cross and Diversity Outbred populations.

Features

• Chromosome lengths:
  • chromsizes(), to which the next two are shortcuts
  • chromsizes_mm9(), old assembly ("build 37"/UCSC mm9)
  • chromsizes_mm10(), current assembly ("build 38"/UCSC mm10)
• Position of the pseudoautosomal boundary (PAR; ie. the part of the X chromosome that might be heterozygous in males):
  • pseudoautosomal_boundary()
  • PAR_mm9()
  • PAR_mm10()
• Strain names and strain codes for the CC/DO founders:
  • cc_strains(), for full strain names ("A/J", "C57BL/6J", ...)
  • CC_STRAINS(), for strain codes (A,B, ...)
• Canonical colour schemes for the CC/DO founders, corresponding to the full strain names or codes:
  • cc_colors()
  • CC_COLORS()
• Canonical colour schemes for subspecies of Mus musuclus and colours for related speices in Mus:
  • mus_taxa()
  • mus_colors()

We also define a set of convience functions using these colour schemes with ggplot2:

• scale_color_cc()
• scale_fill_cc()
• scale_color_mus()
• scale_fill_mus()
• scale_color_sex()
• scale_fill_sex()

Notes

For chromosome names, both the UCSC ("chr1", ..., "chrX", "chrM") and Ensembl ("1", ..., "X","MT") naming conventions are supported. The desired convention is guessed from input arguments: chromsizes("mm10") will return UCSC names, while chromsizes("GRCm38") will return Ensembl names. For users of the Bioconductor stack (especially the GenomicRanges package), they can be returned as a Seqinfo object by passing as.seqinfo = TRUE to any of the chromsizes() family of functions.

A note about "build 37" coordinates: these are provided for backwards compatibility, but users should really consider upgrading to the newer genome assembly.

andrewparkermorgan/mouser documentation built on May 14, 2022, 8:06 p.m.