NEWS.md

In rqtl/qtl2plot: Data Visualization for QTL Experiments

qtl2plot 0.5-18 (2017-11-24)

New features

• plot_coef() now takes an argument legend to control addition of a legend. If NULL, no legend is included. Otherwise it indicates the placement of the legend (for example "topright" or "bottomleft". There are hidden arguments legend_lab for labels and legend_ncol for the number of columns.

• plot_snpasso() now takes a minlod argument; points with LOD less than this value are omitted.

• plot_snpasso() also takes a genes argument. If provided, a two-panel plot is displayed with SNP association results above and gene locations below.

• plot_snpasso() also takes a lodcolumn argument for selecting the column of LOD scores to plot.

• New (hidden) graphics paramater for plot_scan1(), altcol, for having colors alternate between chromosomes, for the case of a Manhattan plot particular of SNP association results.

Minor changes

• Fixed plot_snpasso() so it can handle results for multiple chromosomes.

qtl2plot 0.5-17 (2017-11-08)

New features

• Added function plot_genoprob() for plotting a heat map of the genotype probabilities for a single individual on a single chromosome.

• Added function plot_genoprobcomp() for plotting a bivariate heat map comparing two sets of genotype probabilities for a single individual on a single chromosome.

• Added swap_axes argument to plot_onegeno() (to have the option of chromosomes running horizontally rather than vertically) and to plot_pxg() (to have the option of having genotypes on y-axis and phenotypes horizontally).

Minor changes

• Throughout, changed arguments like hlines.col to use an underscore rather than a period: hlines_col.

• Hid a bunch of graphics parameters, to be passed via ..., so that the function definitions aren't so cluttered.

• For plot_snpasso(), changed arguments drop.hilit and col.hilit to drop_hilit and col_hilit for consistency with other functions' argument names.

qtl2plot 0.5-16 (2017-10-17)

New features

• Added function plot_pxg() for plotting phenotypes versus genotype at a putative QTL.

qtl2plot 0.5-13 (2017-08-04)

Minor changes

• Added arguments to plot_genes to make it more flexible; in particular, to allow differences in column names and to allow start and stop positions to be in either bp or Mbp.

qtl2plot 0.5-12 (2017-07-31)

New features

• Added plot_peaks(), for plotting the locations (and optionally confidence intervals) of inferred QTL.

• Added plot_onegeno() for plotting the genome-wide genotypes for one individual.

qtl2plot 0.5-10 (2017-07-11)

Bug fixes

• Ensure that scan1() output and the map are aligned.

qtl2plot 0.5-7 (2017-06-05)

Minor changes

• Revised installation instructions.

qtl2plot 0.5-6 (2017-04-29)

Minor changes

• Trap cases of the input map being NULL. This happens to me particularly when I try some_cross$pmap but the cross object doesn't contain a physical map.

qtl2plot 0.5-4 (2017-03-11)

Bug fixes

• Fix bug in plot_scan1: need to import qtl2scan::subset_scan1.

qtl2plot 0.5-3 (2017-03-07)

New features

• Refactored to deal with changes in data structures in qtl2geno and qtl2scan.

• Most functions now need you to provide the map of markers/pseudomarkers, produced by insert_pseudomarkers.

• The plot_snpasso function requires the snpinfo as supplemented by index_snps (that is, with the information on which groups of SNPs are equivalent).

rqtl/qtl2plot documentation built on May 28, 2019, 2:36 a.m.