ap_overview: Signal overview

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

Signal overview

Description

Boxplots of signals per antigen and sample in different orders.

Usage

ap_overview(
  x,
  grepneg = "his6abp|hisabp|empty|bare|biotin|neutravidin|neg_",
  greppos = "anti-h|hIg|ebna",
  includeFilter = TRUE,
  Aglabels = "Gene_agID",
  shouldpdf = TRUE,
  filename = "Signal_overview.pdf",
  width = 25,
  height = 15,
  useDingbats = FALSE,
  ...
)

Arguments

x	List with at least one elements, see Deatils for naming and content.
grepneg	Regular expression for color of negative control beads.
greppos	Regular expression for color of positive control beads.
includeFilter	Logical, should antigen boxes be colored based on filtering?
Aglabels	Column in x$BEADS with matching names as columns in x$MFI. Only used if includeFilter is TRUE.
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().
...	Further arguments passed to boxplot().

Details

The x list needs to include at least the element MFI = assay mfi.

BEADS = Beads info. Only needed if includeFilter is TRUE.

Data points with the value NA or 0 will be set to 1 for the plotting to allow for logarithmic scale without filtering any beads or samples.

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

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