architectureplot: Plot data annotated

In danjlawson/robustarchitecture: Estimate Genomic Architecture parameters using robust statistics

Description

Filter data to keep only the top k by proportion of variance explained, which must be provided in a column called 'propexplained'.

Usage

architectureplot(
  dat,
  detail = NULL,
  mycols = c("#AAAAAA44", "#0000FF44", "#FF000044"),
  mar = c(6, 5, 3, 5),
  xlim = c(0.01, 0.5),
  ylim = NULL,
  xlab = "MAF",
  ylab = "Effect magnitude",
  log = "",
  tx = seq(0.005, 0.5, length.out = 100),
  main = "Genomic Architecture structure",
  show.data = TRUE,
  show.bins = TRUE,
  show.res = TRUE,
  data.pch = 19,
  data.cex = 0.5,
  bins.lty = 2,
  res.scale = 1,
  res.lwd = 1,
  res.col = "#008800FF",
  res.shade = "#88FF8844",
  res.lab = "Extreme class proportion",
  res.lab.line = 3,
  res.adj = 0.5,
  ...
)

Arguments

dat	Data frame containing MAF and beta in first two columns.
detail	(Default: NULL) The results of a call to detail; if NULL, the inference with default settings for thresholds and bins are used.,
mycols	(Default: c(grey,blue,red)) three colours, one for each class of SNP
mar	(Default: c(6,5,3,5)) Margins, passed to par(mar=mar) if not NA.
xlim	(Default: c(0.01,0.5)) As provided to plot.
ylim	(Default: NA, meaning use c(0,max(dat[,2])) As provided to plot.
xlab	(Default: "MAF") As provided to plot.
ylab	(Default: "Effect magnitude") As provided to plot.
log	(Default: "") As provided to plot.
tx	(Default: seq(0.005,0.5,length.out=100)) x values to evaluate the architecture curves at
main	(Default: "Genomic Architecture structure") as provided to plot.
show.data	(Default: TRUE) whether to plot the data.
show.bins	(Default: TRUE) whether to plot the bins.
show.res	(Default: TRUE) whether to show the result proportions, if detail provided.
data.pch	(Default: 19) pch for data.
data.cex	(Default: 0.5) cex for data.
bins.lty	(Default: 2) line type of the bin boundaries (if detail provided).
res.scale	(Default: 1) vertical scaling of the results. Set to values < 1 to restrict the class proportion data into the bottom segment, which is often excluded from architecture plots.
res.lwd	(Default: 1) Line width of the class proportion results.
res.col	(Default: "#008800FF" which is dark green) colour for all results to be displayed.
res.shade	(Default: "#88FF8844" which is pale green) colour for the theoretically expected variation in proportions per frequency bin.
res.lab	(Default: "Extreme class proportion") axis label for the results. Written in res.col.
res.lab.line	(Default: 3) line to write res.lab with mtext.
res.adj	(Default:0.5) vertical location to write res.lab. Try setting to 0 if you have used res.scale<1.
...	Additional parameters to plot.

Value

A dataframe the same shape as provided with only the top k SNPs.

danjlawson/robustarchitecture documentation built on Dec. 19, 2021, 8:09 p.m.