Plot RDA results

Plot RDA results

Usage

rda_plot(
  mod,
  rda_snps = NULL,
  pvalues = NULL,
  axes = "all",
  biplot_axes = NULL,
  sig = 0.05,
  manhattan = NULL,
  rdaplot = NULL,
  binwidth = NULL
)

Arguments

mod

model object of class rda; if this is all that's provided, histograms with loadings will be generated

rda_snps

vector of outlier SNPs (defaults to NULL)

pvalues

if creating a Manhattan plot (i.e., manhattan = TRUE), a matrix of p-values (defaults to NULL)

axes

which RDA axes to include while plotting (defaults to "all")

biplot_axes

if creating an RDA biplot (i.e., rdaplot = TRUE), which pairs of axes to plot. Defaults to plotting all pairs of axes possible, otherwise can be set to a single pair of axes (e.g., c(1,2)) or a list of axes pairs (e.g., list(c(1,2), c(2,3))))

sig

if creating a Manhattan plot, significance threshold for y axis (defaults to 0.05)

manhattan

whether to produce Manhattan plot (defaults to TRUE)

rdaplot

whether to produce an RDA biplot (defaults to TRUE). If only one axis is provided, instead of a biplot, a histogram will be created

binwidth

width of bins for histograms (defaults to NULL)

See also

Other RDA functions: rda_cor(), rda_do_everything(), rda_getoutliers(), rda_run(), rda_table(), rda_varpart(), rda_varpart_table()