Visualize site rankings according to mean-squared errors

Source: R/plot_functions.R

Site rankings are visualized

consistencyPlot(
  object,
  var2plot = "rank",
  which.phantom = NULL,
  which.parameter = NULL,
  group.by = NULL,
  which.assay = NULL,
  which.data = "uncalibrated",
  which.plot = "box",
  color.option = "cividis",
  show.tile.value = F
)

Arguments

object

Calibration Object
var2plot

Character indicating which ranking meausre to plot. On of:

  • "rank" - Default

  • "mse" - Normalized mean-squared errors (mse) are plotted.
which.phantom

Specify which phantom to plot rankings for. If unspecified and multiple phantoms exist in dataset, function will return error requesting that specific phantom be specified.
which.parameter

character indicating which parameters to include. If unspecified, all are included.
group.by

Grouping variable
which.assay

Character specifying which assay to identify reference site for.
which.data

Character specifying which data to identify reference site for.
which.plot

One of:

  • "box" - boxplot of site-specific parameter rankings

  • "tile" - Default. heatmap of site-specific parameter rankings
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
show.tile.value

Logical specifying whether to show site rankings, overlaid on heamap (if which.plot == "tile")

Value

Character

See also

identifyReference, consistencyAnalysis