ap_negbeads: Overview of signals in relation to neg control beads

In cekehe/rappp: QC, data transformation and visualization for PAPP

Overview of signals in relation to neg control beads

Description

Plot overview of singals in relation to the neg control beads (Empty, His6ABP, Neutravidin or Biotin). Based on output from Autoimmunity Profiling scoring function ap_scoring2().

Usage

ap_negbeads(
  x,
  center_prob = 0.5,
  shouldpdf = TRUE,
  filename = "neg-control-beads.pdf",
  width = 15,
  height = 10,
  useDingbats = FALSE
)

Arguments

x	List with at least four elements, see Deatils for naming and content.
center_prob	value in [0,1] passed to prob in quantile(), defaults to the median.
shouldpdf	Logical, should it plot to pdf?
filename	String with filename and desired path, end with .pdf
width, height	Width and height for pdf, see pdf().
useDingbats	Logical. Default is FALSE, compared to in default pdf().

Details

The x list needs to include at least the element

MFI = assay mfi, column names of negative control columns should include empty|bare|blank|his6abp|hisabp|neutravidin,

SCORE = scored data, column names of negative control columns should include empty|bare|blank|his6abp|hisabp|neutravidin,

CUTOFF_KEY = Cutoff key as data.frame with cutoff values, scores and colors.

BEADS = Beads info, including a column called "Filtered" with the value "NegControl" for the negative control beads. Any beads with no text (ie. "" or NA) or "NegControl" in such column will be included.

SAMPLES = Sample info, if any should be excluded then these should be annotated in a column called "Filtered". Any samples with no text (ie. "" or NA) in such column will be included.

Note: The function plots to a layout containing three areas.

cekehe/rappp documentation built on May 17, 2022, 8:54 a.m.