plot.ae: Plot an ae object

In LBMC/RAPToR: Real Age Prediction from Transcriptome staging On Reference

Plot an ae object

Description

Plots age estimates of samples with bootstrap confidence intervals.

Usage

## S3 method for class 'ae'
plot(
  x,
  groups = NULL,
  subset = NULL,
  show.boot_estimates = T,
  show.prior = F,
  col = par("fg"),
  color = col,
  col.b = 2,
  col.p = 1,
  col.l = "gray",
  pch = 16,
  cex = 1,
  truncate_name = c("none", "end", "start"),
  sn_len = 10,
  lmar = 10,
  g.line = lmar * 0.75,
  xlim = NULL,
  xlab = NULL,
  main = NULL,
  CIbar.width = 0.1,
  glob.above = F,
  l.pos = "bottomright",
  ...
)

Arguments

x	an ae object, as returned by ae.
groups	a factor with sample categories (e.g. treatment groups).
subset	an index vector of the samples to plot (defaults to all).
show.boot_estimates	logical ; if TRUE (default), shows individual bootstrap estimates as swarms.
show.prior	logical ; if TRUE, shows input prior(s) on the plot.
col, color	the estimate, confidence interval, and label color.
col.b, col.p, col.l	color of bootstrap estimates, priors, and background lines respectively.
pch, cex, xlim	graphical parameters.
truncate_name	whether to truncate displayed sample names from start, end, or not (default).
sn_len	number of characters to keep when truncating sample names.
lmar	left margin value, increase to fit sample names.
g.line	position of the group names (margin line).
xlab	x axis label.
main	plot title.
CIbar.width	the width of the confidence interval bars.
glob.above	logical ; if TRUE, the global estimate is overlayed above all else.
l.pos	position of the legend when show.prior is TRUE, passed on to legend
...	additional arguments passed on to points.

Examples

requireNamespace('wormRef', quietly = TRUE)

# get some samples to stage
samp <- wormRef::Cel_larval$g[,13:15]

# load interpolated reference
r_larv <- prepare_refdata(ref = 'Cel_larval', datapkg = 'wormRef' , n.inter = 200)

# perform age estimate
ae_test <- ae(samp, r_larv)

# check output
summary(ae_test)
plot(ae_test) # plot all sample estimates
plot_cor(ae_test) # plot individual correlation profiles of samples

# get results
ae_test$age.estimates

LBMC/RAPToR documentation built on April 6, 2023, 12:26 p.m.