Multi-variant reproducibility boxplots

Source: R/plot_functions.R

Generates boxplots summarizing results generated during mvp.analysis.

mvpPlot(
  object,
  which.data = "all",
  group.by = NULL,
  which.parameter = NULL,
  which.phantom = NULL,
  which.precision = "all",
  which.analysis = NULL,
  var2plot = "cv",
  which.assay = NULL,
  outliers = T,
  jitter.width = 0.1,
  color.option = "cividis",
  color.begin = 0,
  color.end = 1,
  point.size = 2,
  point.alpha = 1,
  box.alpha = 0.5,
  return.plt.handle = F,
  combine.plots = F,
  combine.ncols = 2,
  show.rms.statistic = F,
  show.legend.flag = T
)

Arguments

object

Calibration Object.
which.data

Character specifying which dataset to plot svp analysis for. One of:

  • "all" - Default

  • "uncalibrated"

  • "calibrated"
group.by

Vector of features to stratify analysis by. If specified, rms-statistic is not overlaid on boxplot.
which.parameter

Character specifying which parameters to plot. If unspecified, all parameters are plotted.
which.phantom

Character specifying which phantoms to plot. If unspecified, all phantoms are plotted.
which.precision

Character specifying which precision errors to plot. One of:

  • "all" - Default. Short and longitudinal, single- and multi-site precision errors

  • "short" - Short-term precision errors only

  • "long" - Longitudinal precision errors only

  • "single" - Single-site precision errors only

  • "multi" - Multi-site precision errors only
which.analysis

Character indicating which mvp.analysis to get results from. If unspecified, available analyses will be used.
var2plot

Character specifying which precision error metric to plot. One of:

  • cv - coefficient of variance

  • std - standard deviation
which.assay

Character specifying which assay to plot.
outliers

Logical specifying whether to omit outliers from analysis
jitter.width

Numerical specifying width of jitter in boxplot. Default is 0.1.
color.option

Character indicating which color map option to use (from viridis palette). One of:

  • "magma" (or "A")

  • "inferno" (or "B")

  • "plasma" (or "C")

  • "viridis" (or "D")

  • "cividis" (or "E") - Default
color.begin

Hue in [0,1] at which the viridis color map begins. Default is 0.
color.end

Hue in [0,1] at which the viridis color map ends. Default is 1.
point.size

Numeric specifying size of scatter plot points.
point.alpha

Numeric [0,1] specifying degree of transparency for points. Default is 1.
box.alpha

Numeric [0,1] specifying degree of transparency for box plots. Default is 0.5.
return.plt.handle

Logical indicating whether list of ggplot handle is returned. Default is false.
combine.plots

Logical indicating whether plots are combined. Default is false.
combine.ncols

Number of columns when combining plots (Only if combine.plot is true). Default is 2.
show.rms.statistic

Logical indicating to overlay RMS statistic (rms-std or rms-cv) on boxplots. Default is false.
show.legend.flag

Logical indicating to show legend

Value

list of ggplot objects (if return.plt.handle is true)

See also

mvpAnalysis