Short-term reproducibility boxplot

Source: R/plot_functions.R

Generates boxplot summarizing results generated during svp.analysis. Additionally, Kruskal-Wallis rank sum test is performed (using group.by variable for data stratification) and p-values are shown for each comparison group.

svpPlot(
  object,
  which.data = "uncalibrated",
  group.by = NULL,
  which.parameter = NULL,
  which.phantom = NULL,
  var2plot = "cv",
  which.assay = NULL,
  outliers = TRUE,
  jitter.width = 0.1,
  color.option = "cividis",
  color.begin = 0,
  color.end = 1,
  point.size = 2,
  point.alpha = 1,
  box.alpha = 0.5,
  txt.size = NULL,
  xlab.direction = NULL,
  xlab.hjust = NULL,
  xlab.vjust = NULL,
  show.p = T,
  color.option.v2 = NULL,
  color.begin.v2 = NULL,
  color.end.v2 = NULL,
  ylim = NULL
)

Arguments

object

Calibration Object.
which.data

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

  • uncalibrated - Default

  • 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 available phantoms are plotted.
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. Default is 2.
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.
txt.size

Numeric specifying size of text
xlab.direction

Numeric specifying direciton (i.e., angle) of x axis labels
xlab.hjust

Horizontal justification of x axis labels; 0 is left-justified, 0.5 is centered, and 1 is right-justified.
xlab.vjust

Vertical justification of x axis labels;
show.p

Logical specifying if p-values for Kruskal-Wallis rank sum test are shown. Default is true.
color.option.v2

Same as color.option, provides additional flexibility to specify color pallete for second grouping variable if length(group.by) == 2. If unspecified, set to color.option.
color.begin.v2

Same as color.begin, provides additional flexibility to specify hue for second grouping variable if length(group.by) == 2. If unspecified, set to color.begin
color.end.v2

Same as color.end, provides additional flexibility to specify hue for second grouping variable if length(group.by) == 2. If unspecified, set to color.end
ylim

Y axis limits. If unspecified, then set automatically.

Value

ggplot object

See also

svpAnalysis